Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/python-cogent/python-cogent_2021.10.12a1+dfsg-1_amd64.buildinfo
Use metasnap for getting required timestamps
Cannot get timestamps from metasnap: 404 (Not Found)
Use snapshot for getting required timestamps
Get source package info: python-cogent=2021.10.12a1+dfsg-1
Source URL: http://snapshot.notset.fr/mr/package/python-cogent/2021.10.12a1+dfsg-1/srcfiles?fileinfo=1
Initialize APT cache
Get binary package info: autoconf=2.71-2
Binary URL: http://snapshot.notset.fr/mr/binary/autoconf/2.71-2/binfiles?fileinfo=1
Get binary package info: automake=1:1.16.5-1
Binary URL: http://snapshot.notset.fr/mr/binary/automake/1:1.16.5-1/binfiles?fileinfo=1
Get binary package info: autopoint=0.21-4
Binary URL: http://snapshot.notset.fr/mr/binary/autopoint/0.21-4/binfiles?fileinfo=1
Get binary package info: autotools-dev=20180224.1+nmu1
Binary URL: http://snapshot.notset.fr/mr/binary/autotools-dev/20180224.1+nmu1/binfiles?fileinfo=1
Get binary package info: base-files=12
Binary URL: http://snapshot.notset.fr/mr/binary/base-files/12/binfiles?fileinfo=1
Get binary package info: base-passwd=3.5.52
Binary URL: http://snapshot.notset.fr/mr/binary/base-passwd/3.5.52/binfiles?fileinfo=1
Get binary package info: bash=5.1-3.1
Binary URL: http://snapshot.notset.fr/mr/binary/bash/5.1-3.1/binfiles?fileinfo=1
Get binary package info: binfmt-support=2.2.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/binfmt-support/2.2.1-1/binfiles?fileinfo=1
Get binary package info: binutils=2.37-8
Binary URL: http://snapshot.notset.fr/mr/binary/binutils/2.37-8/binfiles?fileinfo=1
Get binary package info: binutils-common=2.37-8
Binary URL: http://snapshot.notset.fr/mr/binary/binutils-common/2.37-8/binfiles?fileinfo=1
Get binary package info: binutils-x86-64-linux-gnu=2.37-8
Binary URL: http://snapshot.notset.fr/mr/binary/binutils-x86-64-linux-gnu/2.37-8/binfiles?fileinfo=1
Get binary package info: bsdextrautils=2.37.2-4
Binary URL: http://snapshot.notset.fr/mr/binary/bsdextrautils/2.37.2-4/binfiles?fileinfo=1
Get binary package info: bsdutils=1:2.37.2-4
Binary URL: http://snapshot.notset.fr/mr/binary/bsdutils/1:2.37.2-4/binfiles?fileinfo=1
Get binary package info: build-essential=12.9
Binary URL: http://snapshot.notset.fr/mr/binary/build-essential/12.9/binfiles?fileinfo=1
Get binary package info: bzip2=1.0.8-4
Binary URL: http://snapshot.notset.fr/mr/binary/bzip2/1.0.8-4/binfiles?fileinfo=1
Get binary package info: ca-certificates=20211016
Binary URL: http://snapshot.notset.fr/mr/binary/ca-certificates/20211016/binfiles?fileinfo=1
Get binary package info: coreutils=8.32-4.1
Binary URL: http://snapshot.notset.fr/mr/binary/coreutils/8.32-4.1/binfiles?fileinfo=1
Get binary package info: cpp=4:11.2.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/cpp/4:11.2.0-2/binfiles?fileinfo=1
Get binary package info: cpp-11=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/cpp-11/11.2.0-10/binfiles?fileinfo=1
Get binary package info: cython3=0.29.24-1
Binary URL: http://snapshot.notset.fr/mr/binary/cython3/0.29.24-1/binfiles?fileinfo=1
Get binary package info: dash=0.5.11+git20210903+057cd650a4ed-3
Binary URL: http://snapshot.notset.fr/mr/binary/dash/0.5.11+git20210903+057cd650a4ed-3/binfiles?fileinfo=1
Get binary package info: debconf=1.5.79
Binary URL: http://snapshot.notset.fr/mr/binary/debconf/1.5.79/binfiles?fileinfo=1
Get binary package info: debhelper=13.5.2
Binary URL: http://snapshot.notset.fr/mr/binary/debhelper/13.5.2/binfiles?fileinfo=1
Get binary package info: debianutils=5.5-1
Binary URL: http://snapshot.notset.fr/mr/binary/debianutils/5.5-1/binfiles?fileinfo=1
Get binary package info: dh-autoreconf=20
Binary URL: http://snapshot.notset.fr/mr/binary/dh-autoreconf/20/binfiles?fileinfo=1
Get binary package info: dh-python=5.20211022.1
Binary URL: http://snapshot.notset.fr/mr/binary/dh-python/5.20211022.1/binfiles?fileinfo=1
Get binary package info: dh-strip-nondeterminism=1.12.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/dh-strip-nondeterminism/1.12.0-2/binfiles?fileinfo=1
Get binary package info: diffutils=1:3.7-5
Binary URL: http://snapshot.notset.fr/mr/binary/diffutils/1:3.7-5/binfiles?fileinfo=1
Get binary package info: docutils-common=0.17.1+dfsg-2
Binary URL: http://snapshot.notset.fr/mr/binary/docutils-common/0.17.1+dfsg-2/binfiles?fileinfo=1
Get binary package info: dpkg=1.20.9
Binary URL: http://snapshot.notset.fr/mr/binary/dpkg/1.20.9/binfiles?fileinfo=1
Get binary package info: dpkg-dev=1.20.9
Binary URL: http://snapshot.notset.fr/mr/binary/dpkg-dev/1.20.9/binfiles?fileinfo=1
Get binary package info: dwz=0.14-1
Binary URL: http://snapshot.notset.fr/mr/binary/dwz/0.14-1/binfiles?fileinfo=1
Get binary package info: file=1:5.39-3
Binary URL: http://snapshot.notset.fr/mr/binary/file/1:5.39-3/binfiles?fileinfo=1
Get binary package info: findutils=4.8.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/findutils/4.8.0-1/binfiles?fileinfo=1
Get binary package info: flit=3.0.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/flit/3.0.0-1/binfiles?fileinfo=1
Get binary package info: fonts-lyx=2.3.6-1
Binary URL: http://snapshot.notset.fr/mr/binary/fonts-lyx/2.3.6-1/binfiles?fileinfo=1
Get binary package info: g++=4:11.2.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/g++/4:11.2.0-2/binfiles?fileinfo=1
Get binary package info: g++-11=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/g++-11/11.2.0-10/binfiles?fileinfo=1
Get binary package info: gcc=4:11.2.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/gcc/4:11.2.0-2/binfiles?fileinfo=1
Get binary package info: gcc-11=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/gcc-11/11.2.0-10/binfiles?fileinfo=1
Get binary package info: gcc-11-base=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/gcc-11-base/11.2.0-10/binfiles?fileinfo=1
Get binary package info: gettext=0.21-4
Binary URL: http://snapshot.notset.fr/mr/binary/gettext/0.21-4/binfiles?fileinfo=1
Get binary package info: gettext-base=0.21-4
Binary URL: http://snapshot.notset.fr/mr/binary/gettext-base/0.21-4/binfiles?fileinfo=1
Get binary package info: grep=3.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/grep/3.7-1/binfiles?fileinfo=1
Get binary package info: groff-base=1.22.4-7
Binary URL: http://snapshot.notset.fr/mr/binary/groff-base/1.22.4-7/binfiles?fileinfo=1
Get binary package info: gzip=1.10-4
Binary URL: http://snapshot.notset.fr/mr/binary/gzip/1.10-4/binfiles?fileinfo=1
Get binary package info: hostname=3.23
Binary URL: http://snapshot.notset.fr/mr/binary/hostname/3.23/binfiles?fileinfo=1
Get binary package info: init-system-helpers=1.60
Binary URL: http://snapshot.notset.fr/mr/binary/init-system-helpers/1.60/binfiles?fileinfo=1
Get binary package info: intltool-debian=0.35.0+20060710.5
Binary URL: http://snapshot.notset.fr/mr/binary/intltool-debian/0.35.0+20060710.5/binfiles?fileinfo=1
Get binary package info: libacl1=2.3.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/libacl1/2.3.1-1/binfiles?fileinfo=1
Get binary package info: libarchive-zip-perl=1.68-1
Binary URL: http://snapshot.notset.fr/mr/binary/libarchive-zip-perl/1.68-1/binfiles?fileinfo=1
Get binary package info: libasan6=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libasan6/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libatomic1=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libatomic1/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libattr1=1:2.5.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/libattr1/1:2.5.1-1/binfiles?fileinfo=1
Get binary package info: libaudit-common=1:3.0.6-1
Binary URL: http://snapshot.notset.fr/mr/binary/libaudit-common/1:3.0.6-1/binfiles?fileinfo=1
Get binary package info: libaudit1=1:3.0.6-1
Binary URL: http://snapshot.notset.fr/mr/binary/libaudit1/1:3.0.6-1/binfiles?fileinfo=1
Get binary package info: libbinutils=2.37-8
Binary URL: http://snapshot.notset.fr/mr/binary/libbinutils/2.37-8/binfiles?fileinfo=1
Get binary package info: libblas3=3.10.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/libblas3/3.10.0-1/binfiles?fileinfo=1
Get binary package info: libblkid1=2.37.2-4
Binary URL: http://snapshot.notset.fr/mr/binary/libblkid1/2.37.2-4/binfiles?fileinfo=1
Get binary package info: libbrotli1=1.0.9-2+b2
Binary URL: http://snapshot.notset.fr/mr/binary/libbrotli1/1.0.9-2+b2/binfiles?fileinfo=1
Get binary package info: libbsd0=0.11.3-1
Binary URL: http://snapshot.notset.fr/mr/binary/libbsd0/0.11.3-1/binfiles?fileinfo=1
Get binary package info: libbz2-1.0=1.0.8-4
Binary URL: http://snapshot.notset.fr/mr/binary/libbz2-1.0/1.0.8-4/binfiles?fileinfo=1
Get binary package info: libc-bin=2.32-4
Binary URL: http://snapshot.notset.fr/mr/binary/libc-bin/2.32-4/binfiles?fileinfo=1
Get binary package info: libc-dev-bin=2.32-4
Binary URL: http://snapshot.notset.fr/mr/binary/libc-dev-bin/2.32-4/binfiles?fileinfo=1
Get binary package info: libc6=2.32-4
Binary URL: http://snapshot.notset.fr/mr/binary/libc6/2.32-4/binfiles?fileinfo=1
Get binary package info: libc6-dev=2.32-4
Binary URL: http://snapshot.notset.fr/mr/binary/libc6-dev/2.32-4/binfiles?fileinfo=1
Get binary package info: libcap-ng0=0.7.9-2.2+b1
Binary URL: http://snapshot.notset.fr/mr/binary/libcap-ng0/0.7.9-2.2+b1/binfiles?fileinfo=1
Get binary package info: libcap2=1:2.44-1
Binary URL: http://snapshot.notset.fr/mr/binary/libcap2/1:2.44-1/binfiles?fileinfo=1
Get binary package info: libcc1-0=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libcc1-0/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libcmark-gfm-extensions0=0.29.0.gfm.0-6
Binary URL: http://snapshot.notset.fr/mr/binary/libcmark-gfm-extensions0/0.29.0.gfm.0-6/binfiles?fileinfo=1
Get binary package info: libcmark-gfm0=0.29.0.gfm.0-6
Binary URL: http://snapshot.notset.fr/mr/binary/libcmark-gfm0/0.29.0.gfm.0-6/binfiles?fileinfo=1
Get binary package info: libcom-err2=1.46.4-1
Binary URL: http://snapshot.notset.fr/mr/binary/libcom-err2/1.46.4-1/binfiles?fileinfo=1
Get binary package info: libcrypt-dev=1:4.4.25-2
Binary URL: http://snapshot.notset.fr/mr/binary/libcrypt-dev/1:4.4.25-2/binfiles?fileinfo=1
Get binary package info: libcrypt1=1:4.4.25-2
Binary URL: http://snapshot.notset.fr/mr/binary/libcrypt1/1:4.4.25-2/binfiles?fileinfo=1
Get binary package info: libctf-nobfd0=2.37-8
Binary URL: http://snapshot.notset.fr/mr/binary/libctf-nobfd0/2.37-8/binfiles?fileinfo=1
Get binary package info: libctf0=2.37-8
Binary URL: http://snapshot.notset.fr/mr/binary/libctf0/2.37-8/binfiles?fileinfo=1
Get binary package info: libdb5.3=5.3.28+dfsg1-0.8
Binary URL: http://snapshot.notset.fr/mr/binary/libdb5.3/5.3.28+dfsg1-0.8/binfiles?fileinfo=1
Get binary package info: libdebconfclient0=0.260
Binary URL: http://snapshot.notset.fr/mr/binary/libdebconfclient0/0.260/binfiles?fileinfo=1
Get binary package info: libdebhelper-perl=13.5.2
Binary URL: http://snapshot.notset.fr/mr/binary/libdebhelper-perl/13.5.2/binfiles?fileinfo=1
Get binary package info: libdeflate0=1.8-1
Binary URL: http://snapshot.notset.fr/mr/binary/libdeflate0/1.8-1/binfiles?fileinfo=1
Get binary package info: libdpkg-perl=1.20.9
Binary URL: http://snapshot.notset.fr/mr/binary/libdpkg-perl/1.20.9/binfiles?fileinfo=1
Get binary package info: libedit2=3.1-20210910-1
Binary URL: http://snapshot.notset.fr/mr/binary/libedit2/3.1-20210910-1/binfiles?fileinfo=1
Get binary package info: libelf1=0.185-2
Binary URL: http://snapshot.notset.fr/mr/binary/libelf1/0.185-2/binfiles?fileinfo=1
Get binary package info: libexpat1=2.4.1-3
Binary URL: http://snapshot.notset.fr/mr/binary/libexpat1/2.4.1-3/binfiles?fileinfo=1
Get binary package info: libexpat1-dev=2.4.1-3
Binary URL: http://snapshot.notset.fr/mr/binary/libexpat1-dev/2.4.1-3/binfiles?fileinfo=1
Get binary package info: libffi8=3.4.2-3
Binary URL: http://snapshot.notset.fr/mr/binary/libffi8/3.4.2-3/binfiles?fileinfo=1
Get binary package info: libfile-stripnondeterminism-perl=1.12.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/libfile-stripnondeterminism-perl/1.12.0-2/binfiles?fileinfo=1
Get binary package info: libfreetype6=2.11.0+dfsg-1
Binary URL: http://snapshot.notset.fr/mr/binary/libfreetype6/2.11.0+dfsg-1/binfiles?fileinfo=1
Get binary package info: libfribidi0=1.0.8-2
Binary URL: http://snapshot.notset.fr/mr/binary/libfribidi0/1.0.8-2/binfiles?fileinfo=1
Get binary package info: libgcc-11-dev=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libgcc-11-dev/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libgcc-s1=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libgcc-s1/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libgcrypt20=1.9.4-3+b1
Binary URL: http://snapshot.notset.fr/mr/binary/libgcrypt20/1.9.4-3+b1/binfiles?fileinfo=1
Get binary package info: libgdbm-compat4=1.22-1
Binary URL: http://snapshot.notset.fr/mr/binary/libgdbm-compat4/1.22-1/binfiles?fileinfo=1
Get binary package info: libgdbm6=1.22-1
Binary URL: http://snapshot.notset.fr/mr/binary/libgdbm6/1.22-1/binfiles?fileinfo=1
Get binary package info: libgfortran5=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libgfortran5/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libglib2.0-0=2.70.0-3
Binary URL: http://snapshot.notset.fr/mr/binary/libglib2.0-0/2.70.0-3/binfiles?fileinfo=1
Get binary package info: libgmp10=2:6.2.1+dfsg-2
Binary URL: http://snapshot.notset.fr/mr/binary/libgmp10/2:6.2.1+dfsg-2/binfiles?fileinfo=1
Get binary package info: libgomp1=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libgomp1/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libgpg-error0=1.42-3
Binary URL: http://snapshot.notset.fr/mr/binary/libgpg-error0/1.42-3/binfiles?fileinfo=1
Get binary package info: libgraphite2-3=1.3.14-1
Binary URL: http://snapshot.notset.fr/mr/binary/libgraphite2-3/1.3.14-1/binfiles?fileinfo=1
Get binary package info: libgssapi-krb5-2=1.18.3-7
Binary URL: http://snapshot.notset.fr/mr/binary/libgssapi-krb5-2/1.18.3-7/binfiles?fileinfo=1
Get binary package info: libharfbuzz0b=2.7.4-1
Binary URL: http://snapshot.notset.fr/mr/binary/libharfbuzz0b/2.7.4-1/binfiles?fileinfo=1
Get binary package info: libicu67=67.1-7
Binary URL: http://snapshot.notset.fr/mr/binary/libicu67/67.1-7/binfiles?fileinfo=1
Get binary package info: libimagequant0=2.12.2-1.1
Binary URL: http://snapshot.notset.fr/mr/binary/libimagequant0/2.12.2-1.1/binfiles?fileinfo=1
Get binary package info: libisl23=0.24-2
Binary URL: http://snapshot.notset.fr/mr/binary/libisl23/0.24-2/binfiles?fileinfo=1
Get binary package info: libitm1=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libitm1/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libjbig0=2.1-3.1+b2
Binary URL: http://snapshot.notset.fr/mr/binary/libjbig0/2.1-3.1+b2/binfiles?fileinfo=1
Get binary package info: libjpeg62-turbo=1:2.0.6-4
Binary URL: http://snapshot.notset.fr/mr/binary/libjpeg62-turbo/1:2.0.6-4/binfiles?fileinfo=1
Get binary package info: libjs-jquery=3.5.1+dfsg+~3.5.5-8
Binary URL: http://snapshot.notset.fr/mr/binary/libjs-jquery/3.5.1+dfsg+~3.5.5-8/binfiles?fileinfo=1
Get binary package info: libjs-jquery-ui=1.12.1+dfsg-8
Binary URL: http://snapshot.notset.fr/mr/binary/libjs-jquery-ui/1.12.1+dfsg-8/binfiles?fileinfo=1
Get binary package info: libjs-sphinxdoc=4.2.0-5
Binary URL: http://snapshot.notset.fr/mr/binary/libjs-sphinxdoc/4.2.0-5/binfiles?fileinfo=1
Get binary package info: libjs-underscore=1.9.1~dfsg-4
Binary URL: http://snapshot.notset.fr/mr/binary/libjs-underscore/1.9.1~dfsg-4/binfiles?fileinfo=1
Get binary package info: libk5crypto3=1.18.3-7
Binary URL: http://snapshot.notset.fr/mr/binary/libk5crypto3/1.18.3-7/binfiles?fileinfo=1
Get binary package info: libkeyutils1=1.6.1-2
Binary URL: http://snapshot.notset.fr/mr/binary/libkeyutils1/1.6.1-2/binfiles?fileinfo=1
Get binary package info: libkrb5-3=1.18.3-7
Binary URL: http://snapshot.notset.fr/mr/binary/libkrb5-3/1.18.3-7/binfiles?fileinfo=1
Get binary package info: libkrb5support0=1.18.3-7
Binary URL: http://snapshot.notset.fr/mr/binary/libkrb5support0/1.18.3-7/binfiles?fileinfo=1
Get binary package info: liblapack3=3.10.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/liblapack3/3.10.0-1/binfiles?fileinfo=1
Get binary package info: liblbfgsb0=3.0+dfsg.3-9
Binary URL: http://snapshot.notset.fr/mr/binary/liblbfgsb0/3.0+dfsg.3-9/binfiles?fileinfo=1
Get binary package info: liblcms2-2=2.12~rc1-2
Binary URL: http://snapshot.notset.fr/mr/binary/liblcms2-2/2.12~rc1-2/binfiles?fileinfo=1
Get binary package info: libllvm9=1:9.0.1-20
Binary URL: http://snapshot.notset.fr/mr/binary/libllvm9/1:9.0.1-20/binfiles?fileinfo=1
Get binary package info: liblsan0=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/liblsan0/11.2.0-10/binfiles?fileinfo=1
Get binary package info: liblz4-1=1.9.3-2
Binary URL: http://snapshot.notset.fr/mr/binary/liblz4-1/1.9.3-2/binfiles?fileinfo=1
Get binary package info: liblzma5=5.2.5-2
Binary URL: http://snapshot.notset.fr/mr/binary/liblzma5/5.2.5-2/binfiles?fileinfo=1
Get binary package info: libmagic-mgc=1:5.39-3
Binary URL: http://snapshot.notset.fr/mr/binary/libmagic-mgc/1:5.39-3/binfiles?fileinfo=1
Get binary package info: libmagic1=1:5.39-3
Binary URL: http://snapshot.notset.fr/mr/binary/libmagic1/1:5.39-3/binfiles?fileinfo=1
Get binary package info: libmd0=1.0.4-1
Binary URL: http://snapshot.notset.fr/mr/binary/libmd0/1.0.4-1/binfiles?fileinfo=1
Get binary package info: libmount1=2.37.2-4
Binary URL: http://snapshot.notset.fr/mr/binary/libmount1/2.37.2-4/binfiles?fileinfo=1
Get binary package info: libmpc3=1.2.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/libmpc3/1.2.1-1/binfiles?fileinfo=1
Get binary package info: libmpdec3=2.5.1-2
Binary URL: http://snapshot.notset.fr/mr/binary/libmpdec3/2.5.1-2/binfiles?fileinfo=1
Get binary package info: libmpfr6=4.1.0-3
Binary URL: http://snapshot.notset.fr/mr/binary/libmpfr6/4.1.0-3/binfiles?fileinfo=1
Get binary package info: libncursesw6=6.2+20210905-1
Binary URL: http://snapshot.notset.fr/mr/binary/libncursesw6/6.2+20210905-1/binfiles?fileinfo=1
Get binary package info: libnsl-dev=1.3.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/libnsl-dev/1.3.0-2/binfiles?fileinfo=1
Get binary package info: libnsl2=1.3.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/libnsl2/1.3.0-2/binfiles?fileinfo=1
Get binary package info: libopenjp2-7=2.4.0-3
Binary URL: http://snapshot.notset.fr/mr/binary/libopenjp2-7/2.4.0-3/binfiles?fileinfo=1
Get binary package info: libpam-modules=1.4.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libpam-modules/1.4.0-10/binfiles?fileinfo=1
Get binary package info: libpam-modules-bin=1.4.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libpam-modules-bin/1.4.0-10/binfiles?fileinfo=1
Get binary package info: libpam-runtime=1.4.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libpam-runtime/1.4.0-10/binfiles?fileinfo=1
Get binary package info: libpam0g=1.4.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libpam0g/1.4.0-10/binfiles?fileinfo=1
Get binary package info: libpcre2-8-0=10.36-2
Binary URL: http://snapshot.notset.fr/mr/binary/libpcre2-8-0/10.36-2/binfiles?fileinfo=1
Get binary package info: libpcre3=2:8.39-13
Binary URL: http://snapshot.notset.fr/mr/binary/libpcre3/2:8.39-13/binfiles?fileinfo=1
Get binary package info: libperl5.32=5.32.1-6
Binary URL: http://snapshot.notset.fr/mr/binary/libperl5.32/5.32.1-6/binfiles?fileinfo=1
Get binary package info: libpfm4=4.11.1+git32-gd0b85fb-1
Binary URL: http://snapshot.notset.fr/mr/binary/libpfm4/4.11.1+git32-gd0b85fb-1/binfiles?fileinfo=1
Get binary package info: libpipeline1=1.5.3-1
Binary URL: http://snapshot.notset.fr/mr/binary/libpipeline1/1.5.3-1/binfiles?fileinfo=1
Get binary package info: libpng16-16=1.6.37-3
Binary URL: http://snapshot.notset.fr/mr/binary/libpng16-16/1.6.37-3/binfiles?fileinfo=1
Get binary package info: libpython3-all-dev=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/libpython3-all-dev/3.9.7-1/binfiles?fileinfo=1
Get binary package info: libpython3-dev=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/libpython3-dev/3.9.7-1/binfiles?fileinfo=1
Get binary package info: libpython3-stdlib=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/libpython3-stdlib/3.9.7-1/binfiles?fileinfo=1
Get binary package info: libpython3.9=3.9.7-4
Binary URL: http://snapshot.notset.fr/mr/binary/libpython3.9/3.9.7-4/binfiles?fileinfo=1
Get binary package info: libpython3.9-dev=3.9.7-4
Binary URL: http://snapshot.notset.fr/mr/binary/libpython3.9-dev/3.9.7-4/binfiles?fileinfo=1
Get binary package info: libpython3.9-minimal=3.9.7-4
Binary URL: http://snapshot.notset.fr/mr/binary/libpython3.9-minimal/3.9.7-4/binfiles?fileinfo=1
Get binary package info: libpython3.9-stdlib=3.9.7-4
Binary URL: http://snapshot.notset.fr/mr/binary/libpython3.9-stdlib/3.9.7-4/binfiles?fileinfo=1
Get binary package info: libquadmath0=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libquadmath0/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libraqm0=0.7.0-4
Binary URL: http://snapshot.notset.fr/mr/binary/libraqm0/0.7.0-4/binfiles?fileinfo=1
Get binary package info: libreadline8=8.1-2
Binary URL: http://snapshot.notset.fr/mr/binary/libreadline8/8.1-2/binfiles?fileinfo=1
Get binary package info: libseccomp2=2.5.2-2
Binary URL: http://snapshot.notset.fr/mr/binary/libseccomp2/2.5.2-2/binfiles?fileinfo=1
Get binary package info: libselinux1=3.1-3+b1
Binary URL: http://snapshot.notset.fr/mr/binary/libselinux1/3.1-3+b1/binfiles?fileinfo=1
Get binary package info: libsigsegv2=2.13-1
Binary URL: http://snapshot.notset.fr/mr/binary/libsigsegv2/2.13-1/binfiles?fileinfo=1
Get binary package info: libsmartcols1=2.37.2-4
Binary URL: http://snapshot.notset.fr/mr/binary/libsmartcols1/2.37.2-4/binfiles?fileinfo=1
Get binary package info: libsqlite3-0=3.36.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/libsqlite3-0/3.36.0-2/binfiles?fileinfo=1
Get binary package info: libssl1.1=1.1.1l-1
Binary URL: http://snapshot.notset.fr/mr/binary/libssl1.1/1.1.1l-1/binfiles?fileinfo=1
Get binary package info: libstdc++-11-dev=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libstdc++-11-dev/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libstdc++6=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libstdc++6/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libsub-override-perl=0.09-2
Binary URL: http://snapshot.notset.fr/mr/binary/libsub-override-perl/0.09-2/binfiles?fileinfo=1
Get binary package info: libsystemd0=249.5-2
Binary URL: http://snapshot.notset.fr/mr/binary/libsystemd0/249.5-2/binfiles?fileinfo=1
Get binary package info: libtbb2=2020.3-1
Binary URL: http://snapshot.notset.fr/mr/binary/libtbb2/2020.3-1/binfiles?fileinfo=1
Get binary package info: libtiff5=4.3.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/libtiff5/4.3.0-2/binfiles?fileinfo=1
Get binary package info: libtinfo6=6.2+20210905-1
Binary URL: http://snapshot.notset.fr/mr/binary/libtinfo6/6.2+20210905-1/binfiles?fileinfo=1
Get binary package info: libtirpc-common=1.3.2-2
Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc-common/1.3.2-2/binfiles?fileinfo=1
Get binary package info: libtirpc-dev=1.3.2-2
Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc-dev/1.3.2-2/binfiles?fileinfo=1
Get binary package info: libtirpc3=1.3.2-2
Binary URL: http://snapshot.notset.fr/mr/binary/libtirpc3/1.3.2-2/binfiles?fileinfo=1
Get binary package info: libtool=2.4.6-15
Binary URL: http://snapshot.notset.fr/mr/binary/libtool/2.4.6-15/binfiles?fileinfo=1
Get binary package info: libtsan0=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libtsan0/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libubsan1=11.2.0-10
Binary URL: http://snapshot.notset.fr/mr/binary/libubsan1/11.2.0-10/binfiles?fileinfo=1
Get binary package info: libuchardet0=0.0.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/libuchardet0/0.0.7-1/binfiles?fileinfo=1
Get binary package info: libudev1=249.5-2
Binary URL: http://snapshot.notset.fr/mr/binary/libudev1/249.5-2/binfiles?fileinfo=1
Get binary package info: libunistring2=0.9.10-6
Binary URL: http://snapshot.notset.fr/mr/binary/libunistring2/0.9.10-6/binfiles?fileinfo=1
Get binary package info: libuuid1=2.37.2-4
Binary URL: http://snapshot.notset.fr/mr/binary/libuuid1/2.37.2-4/binfiles?fileinfo=1
Get binary package info: libwebp6=0.6.1-2.1
Binary URL: http://snapshot.notset.fr/mr/binary/libwebp6/0.6.1-2.1/binfiles?fileinfo=1
Get binary package info: libwebpdemux2=0.6.1-2.1
Binary URL: http://snapshot.notset.fr/mr/binary/libwebpdemux2/0.6.1-2.1/binfiles?fileinfo=1
Get binary package info: libwebpmux3=0.6.1-2.1
Binary URL: http://snapshot.notset.fr/mr/binary/libwebpmux3/0.6.1-2.1/binfiles?fileinfo=1
Get binary package info: libxau6=1:1.0.9-1
Binary URL: http://snapshot.notset.fr/mr/binary/libxau6/1:1.0.9-1/binfiles?fileinfo=1
Get binary package info: libxcb1=1.14-3
Binary URL: http://snapshot.notset.fr/mr/binary/libxcb1/1.14-3/binfiles?fileinfo=1
Get binary package info: libxdmcp6=1:1.1.2-3
Binary URL: http://snapshot.notset.fr/mr/binary/libxdmcp6/1:1.1.2-3/binfiles?fileinfo=1
Get binary package info: libxml2=2.9.12+dfsg-5
Binary URL: http://snapshot.notset.fr/mr/binary/libxml2/2.9.12+dfsg-5/binfiles?fileinfo=1
Get binary package info: libz3-4=4.8.12-1+b1
Binary URL: http://snapshot.notset.fr/mr/binary/libz3-4/4.8.12-1+b1/binfiles?fileinfo=1
Get binary package info: libzstd1=1.4.8+dfsg-3
Binary URL: http://snapshot.notset.fr/mr/binary/libzstd1/1.4.8+dfsg-3/binfiles?fileinfo=1
Get binary package info: linux-libc-dev=5.14.12-1
Binary URL: http://snapshot.notset.fr/mr/binary/linux-libc-dev/5.14.12-1/binfiles?fileinfo=1
Get binary package info: llvm-9=1:9.0.1-20
Binary URL: http://snapshot.notset.fr/mr/binary/llvm-9/1:9.0.1-20/binfiles?fileinfo=1
Get binary package info: llvm-9-runtime=1:9.0.1-20
Binary URL: http://snapshot.notset.fr/mr/binary/llvm-9-runtime/1:9.0.1-20/binfiles?fileinfo=1
Get binary package info: login=1:4.8.1-1.1
Binary URL: http://snapshot.notset.fr/mr/binary/login/1:4.8.1-1.1/binfiles?fileinfo=1
Get binary package info: lsb-base=11.1.0
Binary URL: http://snapshot.notset.fr/mr/binary/lsb-base/11.1.0/binfiles?fileinfo=1
Get binary package info: m4=1.4.18-5
Binary URL: http://snapshot.notset.fr/mr/binary/m4/1.4.18-5/binfiles?fileinfo=1
Get binary package info: mailcap=3.70
Binary URL: http://snapshot.notset.fr/mr/binary/mailcap/3.70/binfiles?fileinfo=1
Get binary package info: make=4.3-4.1
Binary URL: http://snapshot.notset.fr/mr/binary/make/4.3-4.1/binfiles?fileinfo=1
Get binary package info: man-db=2.9.4-2
Binary URL: http://snapshot.notset.fr/mr/binary/man-db/2.9.4-2/binfiles?fileinfo=1
Get binary package info: mawk=1.3.4.20200120-2
Binary URL: http://snapshot.notset.fr/mr/binary/mawk/1.3.4.20200120-2/binfiles?fileinfo=1
Get binary package info: media-types=4.0.0
Binary URL: http://snapshot.notset.fr/mr/binary/media-types/4.0.0/binfiles?fileinfo=1
Get binary package info: mime-support=3.66
Binary URL: http://snapshot.notset.fr/mr/binary/mime-support/3.66/binfiles?fileinfo=1
Get binary package info: ncurses-base=6.2+20210905-1
Binary URL: http://snapshot.notset.fr/mr/binary/ncurses-base/6.2+20210905-1/binfiles?fileinfo=1
Get binary package info: ncurses-bin=6.2+20210905-1
Binary URL: http://snapshot.notset.fr/mr/binary/ncurses-bin/6.2+20210905-1/binfiles?fileinfo=1
Get binary package info: openssl=1.1.1l-1
Binary URL: http://snapshot.notset.fr/mr/binary/openssl/1.1.1l-1/binfiles?fileinfo=1
Get binary package info: pandoc=2.9.2.1-1+b2
Binary URL: http://snapshot.notset.fr/mr/binary/pandoc/2.9.2.1-1+b2/binfiles?fileinfo=1
Get binary package info: pandoc-data=2.9.2.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/pandoc-data/2.9.2.1-1/binfiles?fileinfo=1
Get binary package info: patch=2.7.6-7
Binary URL: http://snapshot.notset.fr/mr/binary/patch/2.7.6-7/binfiles?fileinfo=1
Get binary package info: perl=5.32.1-6
Binary URL: http://snapshot.notset.fr/mr/binary/perl/5.32.1-6/binfiles?fileinfo=1
Get binary package info: perl-base=5.32.1-6
Binary URL: http://snapshot.notset.fr/mr/binary/perl-base/5.32.1-6/binfiles?fileinfo=1
Get binary package info: perl-modules-5.32=5.32.1-6
Binary URL: http://snapshot.notset.fr/mr/binary/perl-modules-5.32/5.32.1-6/binfiles?fileinfo=1
Get binary package info: po-debconf=1.0.21+nmu1
Binary URL: http://snapshot.notset.fr/mr/binary/po-debconf/1.0.21+nmu1/binfiles?fileinfo=1
Get binary package info: python-babel-localedata=2.8.0+dfsg.1-7
Binary URL: http://snapshot.notset.fr/mr/binary/python-babel-localedata/2.8.0+dfsg.1-7/binfiles?fileinfo=1
Get binary package info: python-matplotlib-data=3.3.4-2
Binary URL: http://snapshot.notset.fr/mr/binary/python-matplotlib-data/3.3.4-2/binfiles?fileinfo=1
Get binary package info: python3=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3/3.9.7-1/binfiles?fileinfo=1
Get binary package info: python3-alabaster=0.7.12-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-alabaster/0.7.12-1/binfiles?fileinfo=1
Get binary package info: python3-all=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-all/3.9.7-1/binfiles?fileinfo=1
Get binary package info: python3-all-dev=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-all-dev/3.9.7-1/binfiles?fileinfo=1
Get binary package info: python3-attr=20.3.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-attr/20.3.0-1/binfiles?fileinfo=1
Get binary package info: python3-babel=2.8.0+dfsg.1-7
Binary URL: http://snapshot.notset.fr/mr/binary/python3-babel/2.8.0+dfsg.1-7/binfiles?fileinfo=1
Get binary package info: python3-bleach=4.1.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-bleach/4.1.0-1/binfiles?fileinfo=1
Get binary package info: python3-certifi=2020.6.20-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-certifi/2020.6.20-1/binfiles?fileinfo=1
Get binary package info: python3-chardet=4.0.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-chardet/4.0.0-1/binfiles?fileinfo=1
Get binary package info: python3-cycler=0.11.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-cycler/0.11.0-1/binfiles?fileinfo=1
Get binary package info: python3-dateutil=2.8.1-6
Binary URL: http://snapshot.notset.fr/mr/binary/python3-dateutil/2.8.1-6/binfiles?fileinfo=1
Get binary package info: python3-decorator=4.4.2-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-decorator/4.4.2-2/binfiles?fileinfo=1
Get binary package info: python3-defusedxml=0.7.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-defusedxml/0.7.1-1/binfiles?fileinfo=1
Get binary package info: python3-dev=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-dev/3.9.7-1/binfiles?fileinfo=1
Get binary package info: python3-distutils=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-distutils/3.9.7-1/binfiles?fileinfo=1
Get binary package info: python3-docutils=0.17.1+dfsg-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-docutils/0.17.1+dfsg-2/binfiles?fileinfo=1
Get binary package info: python3-entrypoints=0.3-8
Binary URL: http://snapshot.notset.fr/mr/binary/python3-entrypoints/0.3-8/binfiles?fileinfo=1
Get binary package info: python3-html5lib=1.1-3
Binary URL: http://snapshot.notset.fr/mr/binary/python3-html5lib/1.1-3/binfiles?fileinfo=1
Get binary package info: python3-idna=2.10-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-idna/2.10-1/binfiles?fileinfo=1
Get binary package info: python3-imagesize=1.2.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-imagesize/1.2.0-2/binfiles?fileinfo=1
Get binary package info: python3-importlib-metadata=4.6.4-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-importlib-metadata/4.6.4-1/binfiles?fileinfo=1
Get binary package info: python3-iniconfig=1.1.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-iniconfig/1.1.1-1/binfiles?fileinfo=1
Get binary package info: python3-ipython-genutils=0.2.0-5
Binary URL: http://snapshot.notset.fr/mr/binary/python3-ipython-genutils/0.2.0-5/binfiles?fileinfo=1
Get binary package info: python3-jinja2=3.0.1-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-jinja2/3.0.1-2/binfiles?fileinfo=1
Get binary package info: python3-jsonschema=3.2.0-3
Binary URL: http://snapshot.notset.fr/mr/binary/python3-jsonschema/3.2.0-3/binfiles?fileinfo=1
Get binary package info: python3-jupyter-core=4.9.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-jupyter-core/4.9.1-1/binfiles?fileinfo=1
Get binary package info: python3-kiwisolver=1.3.2-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-kiwisolver/1.3.2-1/binfiles?fileinfo=1
Get binary package info: python3-lib2to3=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-lib2to3/3.9.7-1/binfiles?fileinfo=1
Get binary package info: python3-llvmlite=0.35.0-3
Binary URL: http://snapshot.notset.fr/mr/binary/python3-llvmlite/0.35.0-3/binfiles?fileinfo=1
Get binary package info: python3-markupsafe=2.0.1-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-markupsafe/2.0.1-2/binfiles?fileinfo=1
Get binary package info: python3-matplotlib=3.3.4-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-matplotlib/3.3.4-2/binfiles?fileinfo=1
Get binary package info: python3-minimal=3.9.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-minimal/3.9.7-1/binfiles?fileinfo=1
Get binary package info: python3-mistune=0.8.4-5
Binary URL: http://snapshot.notset.fr/mr/binary/python3-mistune/0.8.4-5/binfiles?fileinfo=1
Get binary package info: python3-more-itertools=4.2.0-3
Binary URL: http://snapshot.notset.fr/mr/binary/python3-more-itertools/4.2.0-3/binfiles?fileinfo=1
Get binary package info: python3-nbconvert=5.6.1-3
Binary URL: http://snapshot.notset.fr/mr/binary/python3-nbconvert/5.6.1-3/binfiles?fileinfo=1
Get binary package info: python3-nbformat=5.1.3-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-nbformat/5.1.3-1/binfiles?fileinfo=1
Get binary package info: python3-nbsphinx=0.8.7+ds-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-nbsphinx/0.8.7+ds-1/binfiles?fileinfo=1
Get binary package info: python3-numba=0.52.0-5
Binary URL: http://snapshot.notset.fr/mr/binary/python3-numba/0.52.0-5/binfiles?fileinfo=1
Get binary package info: python3-numpy=1:1.19.5-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-numpy/1:1.19.5-1/binfiles?fileinfo=1
Get binary package info: python3-numpydoc=1.1.0-3
Binary URL: http://snapshot.notset.fr/mr/binary/python3-numpydoc/1.1.0-3/binfiles?fileinfo=1
Get binary package info: python3-packaging=21.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-packaging/21.0-1/binfiles?fileinfo=1
Get binary package info: python3-pandas=1.1.5+dfsg-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pandas/1.1.5+dfsg-2/binfiles?fileinfo=1
Get binary package info: python3-pandas-lib=1.1.5+dfsg-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pandas-lib/1.1.5+dfsg-2/binfiles?fileinfo=1
Get binary package info: python3-pandocfilters=1.4.3-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pandocfilters/1.4.3-1/binfiles?fileinfo=1
Get binary package info: python3-pil=8.3.2-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pil/8.3.2-1/binfiles?fileinfo=1
Get binary package info: python3-pkg-resources=58.2.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pkg-resources/58.2.0-1/binfiles?fileinfo=1
Get binary package info: python3-pluggy=0.13.0-7.1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pluggy/0.13.0-7.1/binfiles?fileinfo=1
Get binary package info: python3-py=1.10.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-py/1.10.0-1/binfiles?fileinfo=1
Get binary package info: python3-pygments=2.7.1+dfsg-2.1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pygments/2.7.1+dfsg-2.1/binfiles?fileinfo=1
Get binary package info: python3-pyparsing=2.4.7-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pyparsing/2.4.7-1/binfiles?fileinfo=1
Get binary package info: python3-pyrsistent=0.15.5-1+b3
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pyrsistent/0.15.5-1+b3/binfiles?fileinfo=1
Get binary package info: python3-pytest=6.2.5-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pytest/6.2.5-1/binfiles?fileinfo=1
Get binary package info: python3-pytoml=0.1.21-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-pytoml/0.1.21-1/binfiles?fileinfo=1
Get binary package info: python3-requests=2.25.1+dfsg-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-requests/2.25.1+dfsg-2/binfiles?fileinfo=1
Get binary package info: python3-roman=3.3-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-roman/3.3-1/binfiles?fileinfo=1
Get binary package info: python3-scipy=1.7.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-scipy/1.7.1-1/binfiles?fileinfo=1
Get binary package info: python3-scitrack=2021.5.3-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-scitrack/2021.5.3-1/binfiles?fileinfo=1
Get binary package info: python3-setuptools=58.2.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-setuptools/58.2.0-1/binfiles?fileinfo=1
Get binary package info: python3-six=1.16.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-six/1.16.0-2/binfiles?fileinfo=1
Get binary package info: python3-snowballstemmer=2.1.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-snowballstemmer/2.1.0-2/binfiles?fileinfo=1
Get binary package info: python3-sphinx=4.2.0-5
Binary URL: http://snapshot.notset.fr/mr/binary/python3-sphinx/4.2.0-5/binfiles?fileinfo=1
Get binary package info: python3-sphinx-bootstrap-theme=0.8.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-sphinx-bootstrap-theme/0.8.0-1/binfiles?fileinfo=1
Get binary package info: python3-sphinx-gallery=0.10.0-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-sphinx-gallery/0.10.0-1/binfiles?fileinfo=1
Get binary package info: python3-testpath=0.5.0+dfsg-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-testpath/0.5.0+dfsg-1/binfiles?fileinfo=1
Get binary package info: python3-tinydb=3.15.2-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-tinydb/3.15.2-2/binfiles?fileinfo=1
Get binary package info: python3-toml=0.10.2-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-toml/0.10.2-1/binfiles?fileinfo=1
Get binary package info: python3-tqdm=4.57.0-2
Binary URL: http://snapshot.notset.fr/mr/binary/python3-tqdm/4.57.0-2/binfiles?fileinfo=1
Get binary package info: python3-traitlets=5.1.1-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-traitlets/5.1.1-1/binfiles?fileinfo=1
Get binary package info: python3-tz=2021.3-1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-tz/2021.3-1/binfiles?fileinfo=1
Get binary package info: python3-urllib3=1.26.5-1~exp1
Binary URL: http://snapshot.notset.fr/mr/binary/python3-urllib3/1.26.5-1~exp1/binfiles?fileinfo=1
Get binary package info: python3-webencodings=0.5.1-4
Binary URL: http://snapshot.notset.fr/mr/binary/python3-webencodings/0.5.1-4/binfiles?fileinfo=1
Get binary package info: python3-zipp=1.0.0-3
Binary URL: http://snapshot.notset.fr/mr/binary/python3-zipp/1.0.0-3/binfiles?fileinfo=1
Get binary package info: python3.9=3.9.7-4
Binary URL: http://snapshot.notset.fr/mr/binary/python3.9/3.9.7-4/binfiles?fileinfo=1
Get binary package info: python3.9-dev=3.9.7-4
Binary URL: http://snapshot.notset.fr/mr/binary/python3.9-dev/3.9.7-4/binfiles?fileinfo=1
Get binary package info: python3.9-minimal=3.9.7-4
Binary URL: http://snapshot.notset.fr/mr/binary/python3.9-minimal/3.9.7-4/binfiles?fileinfo=1
Get binary package info: readline-common=8.1-2
Binary URL: http://snapshot.notset.fr/mr/binary/readline-common/8.1-2/binfiles?fileinfo=1
Get binary package info: rpcsvc-proto=1.4.2-4
Binary URL: http://snapshot.notset.fr/mr/binary/rpcsvc-proto/1.4.2-4/binfiles?fileinfo=1
Get binary package info: sed=4.8-1
Binary URL: http://snapshot.notset.fr/mr/binary/sed/4.8-1/binfiles?fileinfo=1
Get binary package info: sensible-utils=0.0.17
Binary URL: http://snapshot.notset.fr/mr/binary/sensible-utils/0.0.17/binfiles?fileinfo=1
Get binary package info: sgml-base=1.30
Binary URL: http://snapshot.notset.fr/mr/binary/sgml-base/1.30/binfiles?fileinfo=1
Get binary package info: sphinx-common=4.2.0-5
Binary URL: http://snapshot.notset.fr/mr/binary/sphinx-common/4.2.0-5/binfiles?fileinfo=1
Get binary package info: sysvinit-utils=3.00-1
Binary URL: http://snapshot.notset.fr/mr/binary/sysvinit-utils/3.00-1/binfiles?fileinfo=1
Get binary package info: tar=1.34+dfsg-1
Binary URL: http://snapshot.notset.fr/mr/binary/tar/1.34+dfsg-1/binfiles?fileinfo=1
Get binary package info: ttf-bitstream-vera=1.10-8.1
Binary URL: http://snapshot.notset.fr/mr/binary/ttf-bitstream-vera/1.10-8.1/binfiles?fileinfo=1
Get binary package info: tzdata=2021e-1
Binary URL: http://snapshot.notset.fr/mr/binary/tzdata/2021e-1/binfiles?fileinfo=1
Get binary package info: util-linux=2.37.2-4
Binary URL: http://snapshot.notset.fr/mr/binary/util-linux/2.37.2-4/binfiles?fileinfo=1
Get binary package info: xml-core=0.18+nmu1
Binary URL: http://snapshot.notset.fr/mr/binary/xml-core/0.18+nmu1/binfiles?fileinfo=1
Get binary package info: xz-utils=5.2.5-2
Binary URL: http://snapshot.notset.fr/mr/binary/xz-utils/5.2.5-2/binfiles?fileinfo=1
Get binary package info: zlib1g=1:1.2.11.dfsg-2
Binary URL: http://snapshot.notset.fr/mr/binary/zlib1g/1:1.2.11.dfsg-2/binfiles?fileinfo=1
Get binary package info: zlib1g-dev=1:1.2.11.dfsg-2
Binary URL: http://snapshot.notset.fr/mr/binary/zlib1g-dev/1:1.2.11.dfsg-2/binfiles?fileinfo=1
Remaining packages to be found: 300
Timestamp source (114 packages): deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211025T025314Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211108T025858Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210922T025414Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210929T025048Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211103T025035Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210816T024705Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211016T025026Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210902T030735Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210830T143924Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210928T151606Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210827T030044Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211023T025408Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211105T024921Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211012T024642Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211030T025126Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211026T024934Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211003T024803Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211008T024925Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210823T024636Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210908T025933Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210828T025147Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211107T031827Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210926T025629Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211016T210235Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210901T090918Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211014T085745Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211014T215029Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210822T144048Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210906T024530Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211022T024712Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211005T145527Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211015T025547Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211027T025227Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210824T024320Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211012T084840Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210911T144836Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210930T025245Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210909T025907Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210903T030245Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210821T024315Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211021T084416Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211030T160902Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211017T024714Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211029T033902Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210920T025100Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211019T025145Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211009T024746Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211030T084351Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211006T084856Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210822T023545Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210923T145517Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210919T145255Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210826T025527Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211004T030201Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211109T030457Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210911T034835Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211109T145553Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210822T204137Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211102T034943Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211024T145651Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211015T150402Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211028T024824Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211025T145618Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210820T024246Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210923T024950Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211021T025114Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210928T025308Z/ bookworm main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211102T205550Z/ unstable main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210910T030709Z/ unstable main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211016T210235Z/ unstable main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20210919T024804Z/ unstable main
Skipping snapshot: deb http://snapshot.notset.fr/archive/debian/20211023T025408Z/ unstable main
Remaining packages to be found: 1
Timestamp source (1 packages): deb http://snapshot.notset.fr/archive/debian/20211014T155334Z/ unstable main
New buildinfo file: /tmp/python-cogent-2021.10.12a1+dfsg-1c54l8p6r/python-cogent_2021.10.12a1+dfsg-1_amd64.buildinfo
env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf:all=2.71-2 automake:all=1:1.16.5-1 autopoint:all=0.21-4 autotools-dev:all=20180224.1+nmu1 base-files:amd64=12 base-passwd:amd64=3.5.52 bash:amd64=5.1-3.1 binfmt-support:amd64=2.2.1-1 binutils:amd64=2.37-8 binutils-common:amd64=2.37-8 binutils-x86-64-linux-gnu:amd64=2.37-8 bsdextrautils:amd64=2.37.2-4 bsdutils:amd64=1:2.37.2-4 build-essential:amd64=12.9 bzip2:amd64=1.0.8-4 ca-certificates:all=20211016 coreutils:amd64=8.32-4.1 cpp:amd64=4:11.2.0-2 cpp-11:amd64=11.2.0-10 cython3:amd64=0.29.24-1 dash:amd64=0.5.11+git20210903+057cd650a4ed-3 debconf:all=1.5.79 debhelper:all=13.5.2 debianutils:amd64=5.5-1 dh-autoreconf:all=20 dh-python:all=5.20211022.1 dh-strip-nondeterminism:all=1.12.0-2 diffutils:amd64=1:3.7-5 docutils-common:all=0.17.1+dfsg-2 dpkg:amd64=1.20.9 dpkg-dev:all=1.20.9 dwz:amd64=0.14-1 file:amd64=1:5.39-3 findutils:amd64=4.8.0-1 flit:all=3.0.0-1 fonts-lyx:all=2.3.6-1 g++:amd64=4:11.2.0-2 g++-11:amd64=11.2.0-10 gcc:amd64=4:11.2.0-2 gcc-11:amd64=11.2.0-10 gcc-11-base:amd64=11.2.0-10 gettext:amd64=0.21-4 gettext-base:amd64=0.21-4 grep:amd64=3.7-1 groff-base:amd64=1.22.4-7 gzip:amd64=1.10-4 hostname:amd64=3.23 init-system-helpers:all=1.60 intltool-debian:all=0.35.0+20060710.5 libacl1:amd64=2.3.1-1 libarchive-zip-perl:all=1.68-1 libasan6:amd64=11.2.0-10 libatomic1:amd64=11.2.0-10 libattr1:amd64=1:2.5.1-1 libaudit-common:all=1:3.0.6-1 libaudit1:amd64=1:3.0.6-1 libbinutils:amd64=2.37-8 libblas3:amd64=3.10.0-1 libblkid1:amd64=2.37.2-4 libbrotli1:amd64=1.0.9-2+b2 libbsd0:amd64=0.11.3-1 libbz2-1.0:amd64=1.0.8-4 libc-bin:amd64=2.32-4 libc-dev-bin:amd64=2.32-4 libc6:amd64=2.32-4 libc6-dev:amd64=2.32-4 libcap-ng0:amd64=0.7.9-2.2+b1 libcap2:amd64=1:2.44-1 libcc1-0:amd64=11.2.0-10 libcmark-gfm-extensions0:amd64=0.29.0.gfm.0-6 libcmark-gfm0:amd64=0.29.0.gfm.0-6 libcom-err2:amd64=1.46.4-1 libcrypt-dev:amd64=1:4.4.25-2 libcrypt1:amd64=1:4.4.25-2 libctf-nobfd0:amd64=2.37-8 libctf0:amd64=2.37-8 libdb5.3:amd64=5.3.28+dfsg1-0.8 libdebconfclient0:amd64=0.260 libdebhelper-perl:all=13.5.2 libdeflate0:amd64=1.8-1 libdpkg-perl:all=1.20.9 libedit2:amd64=3.1-20210910-1 libelf1:amd64=0.185-2 libexpat1:amd64=2.4.1-3 libexpat1-dev:amd64=2.4.1-3 libffi8:amd64=3.4.2-3 libfile-stripnondeterminism-perl:all=1.12.0-2 libfreetype6:amd64=2.11.0+dfsg-1 libfribidi0:amd64=1.0.8-2 libgcc-11-dev:amd64=11.2.0-10 libgcc-s1:amd64=11.2.0-10 libgcrypt20:amd64=1.9.4-3+b1 libgdbm-compat4:amd64=1.22-1 libgdbm6:amd64=1.22-1 libgfortran5:amd64=11.2.0-10 libglib2.0-0:amd64=2.70.0-3 libgmp10:amd64=2:6.2.1+dfsg-2 libgomp1:amd64=11.2.0-10 libgpg-error0:amd64=1.42-3 libgraphite2-3:amd64=1.3.14-1 libgssapi-krb5-2:amd64=1.18.3-7 libharfbuzz0b:amd64=2.7.4-1 libicu67:amd64=67.1-7 libimagequant0:amd64=2.12.2-1.1 libisl23:amd64=0.24-2 libitm1:amd64=11.2.0-10 libjbig0:amd64=2.1-3.1+b2 libjpeg62-turbo:amd64=1:2.0.6-4 libjs-jquery:all=3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui:all=1.12.1+dfsg-8 libjs-sphinxdoc:all=4.2.0-5 libjs-underscore:all=1.9.1~dfsg-4 libk5crypto3:amd64=1.18.3-7 libkeyutils1:amd64=1.6.1-2 libkrb5-3:amd64=1.18.3-7 libkrb5support0:amd64=1.18.3-7 liblapack3:amd64=3.10.0-1 liblbfgsb0:amd64=3.0+dfsg.3-9 liblcms2-2:amd64=2.12~rc1-2 libllvm9:amd64=1:9.0.1-20 liblsan0:amd64=11.2.0-10 liblz4-1:amd64=1.9.3-2 liblzma5:amd64=5.2.5-2 libmagic-mgc:amd64=1:5.39-3 libmagic1:amd64=1:5.39-3 libmd0:amd64=1.0.4-1 libmount1:amd64=2.37.2-4 libmpc3:amd64=1.2.1-1 libmpdec3:amd64=2.5.1-2 libmpfr6:amd64=4.1.0-3 libncursesw6:amd64=6.2+20210905-1 libnsl-dev:amd64=1.3.0-2 libnsl2:amd64=1.3.0-2 libopenjp2-7:amd64=2.4.0-3 libpam-modules:amd64=1.4.0-10 libpam-modules-bin:amd64=1.4.0-10 libpam-runtime:all=1.4.0-10 libpam0g:amd64=1.4.0-10 libpcre2-8-0:amd64=10.36-2 libpcre3:amd64=2:8.39-13 libperl5.32:amd64=5.32.1-6 libpfm4:amd64=4.11.1+git32-gd0b85fb-1 libpipeline1:amd64=1.5.3-1 libpng16-16:amd64=1.6.37-3 libpython3-all-dev:amd64=3.9.7-1 libpython3-dev:amd64=3.9.7-1 libpython3-stdlib:amd64=3.9.7-1 libpython3.9:amd64=3.9.7-4 libpython3.9-dev:amd64=3.9.7-4 libpython3.9-minimal:amd64=3.9.7-4 libpython3.9-stdlib:amd64=3.9.7-4 libquadmath0:amd64=11.2.0-10 libraqm0:amd64=0.7.0-4 libreadline8:amd64=8.1-2 libseccomp2:amd64=2.5.2-2 libselinux1:amd64=3.1-3+b1 libsigsegv2:amd64=2.13-1 libsmartcols1:amd64=2.37.2-4 libsqlite3-0:amd64=3.36.0-2 libssl1.1:amd64=1.1.1l-1 libstdc++-11-dev:amd64=11.2.0-10 libstdc++6:amd64=11.2.0-10 libsub-override-perl:all=0.09-2 libsystemd0:amd64=249.5-2 libtbb2:amd64=2020.3-1 libtiff5:amd64=4.3.0-2 libtinfo6:amd64=6.2+20210905-1 libtirpc-common:all=1.3.2-2 libtirpc-dev:amd64=1.3.2-2 libtirpc3:amd64=1.3.2-2 libtool:all=2.4.6-15 libtsan0:amd64=11.2.0-10 libubsan1:amd64=11.2.0-10 libuchardet0:amd64=0.0.7-1 libudev1:amd64=249.5-2 libunistring2:amd64=0.9.10-6 libuuid1:amd64=2.37.2-4 libwebp6:amd64=0.6.1-2.1 libwebpdemux2:amd64=0.6.1-2.1 libwebpmux3:amd64=0.6.1-2.1 libxau6:amd64=1:1.0.9-1 libxcb1:amd64=1.14-3 libxdmcp6:amd64=1:1.1.2-3 libxml2:amd64=2.9.12+dfsg-5 libz3-4:amd64=4.8.12-1+b1 libzstd1:amd64=1.4.8+dfsg-3 linux-libc-dev:amd64=5.14.12-1 llvm-9:amd64=1:9.0.1-20 llvm-9-runtime:amd64=1:9.0.1-20 login:amd64=1:4.8.1-1.1 lsb-base:all=11.1.0 m4:amd64=1.4.18-5 mailcap:all=3.70 make:amd64=4.3-4.1 man-db:amd64=2.9.4-2 mawk:amd64=1.3.4.20200120-2 media-types:all=4.0.0 mime-support:all=3.66 ncurses-base:all=6.2+20210905-1 ncurses-bin:amd64=6.2+20210905-1 openssl:amd64=1.1.1l-1 pandoc:amd64=2.9.2.1-1+b2 pandoc-data:all=2.9.2.1-1 patch:amd64=2.7.6-7 perl:amd64=5.32.1-6 perl-base:amd64=5.32.1-6 perl-modules-5.32:all=5.32.1-6 po-debconf:all=1.0.21+nmu1 python-babel-localedata:all=2.8.0+dfsg.1-7 python-matplotlib-data:all=3.3.4-2 python3:amd64=3.9.7-1 python3-alabaster:all=0.7.12-1 python3-all:amd64=3.9.7-1 python3-all-dev:amd64=3.9.7-1 python3-attr:all=20.3.0-1 python3-babel:all=2.8.0+dfsg.1-7 python3-bleach:all=4.1.0-1 python3-certifi:all=2020.6.20-1 python3-chardet:all=4.0.0-1 python3-cycler:all=0.11.0-1 python3-dateutil:all=2.8.1-6 python3-decorator:all=4.4.2-2 python3-defusedxml:all=0.7.1-1 python3-dev:amd64=3.9.7-1 python3-distutils:all=3.9.7-1 python3-docutils:all=0.17.1+dfsg-2 python3-entrypoints:all=0.3-8 python3-html5lib:all=1.1-3 python3-idna:all=2.10-1 python3-imagesize:all=1.2.0-2 python3-importlib-metadata:all=4.6.4-1 python3-iniconfig:all=1.1.1-1 python3-ipython-genutils:all=0.2.0-5 python3-jinja2:all=3.0.1-2 python3-jsonschema:all=3.2.0-3 python3-jupyter-core:all=4.9.1-1 python3-kiwisolver:amd64=1.3.2-1 python3-lib2to3:all=3.9.7-1 python3-llvmlite:amd64=0.35.0-3 python3-markupsafe:amd64=2.0.1-2 python3-matplotlib:amd64=3.3.4-2 python3-minimal:amd64=3.9.7-1 python3-mistune:all=0.8.4-5 python3-more-itertools:all=4.2.0-3 python3-nbconvert:all=5.6.1-3 python3-nbformat:all=5.1.3-1 python3-nbsphinx:all=0.8.7+ds-1 python3-numba:amd64=0.52.0-5 python3-numpy:amd64=1:1.19.5-1 python3-numpydoc:all=1.1.0-3 python3-packaging:all=21.0-1 python3-pandas:all=1.1.5+dfsg-2 python3-pandas-lib:amd64=1.1.5+dfsg-2 python3-pandocfilters:all=1.4.3-1 python3-pil:amd64=8.3.2-1 python3-pkg-resources:all=58.2.0-1 python3-pluggy:all=0.13.0-7.1 python3-py:all=1.10.0-1 python3-pygments:all=2.7.1+dfsg-2.1 python3-pyparsing:all=2.4.7-1 python3-pyrsistent:amd64=0.15.5-1+b3 python3-pytest:all=6.2.5-1 python3-pytoml:all=0.1.21-1 python3-requests:all=2.25.1+dfsg-2 python3-roman:all=3.3-1 python3-scipy:amd64=1.7.1-1 python3-scitrack:all=2021.5.3-1 python3-setuptools:all=58.2.0-1 python3-six:all=1.16.0-2 python3-snowballstemmer:all=2.1.0-2 python3-sphinx:all=4.2.0-5 python3-sphinx-bootstrap-theme:all=0.8.0-1 python3-sphinx-gallery:all=0.10.0-1 python3-testpath:all=0.5.0+dfsg-1 python3-tinydb:all=3.15.2-2 python3-toml:all=0.10.2-1 python3-tqdm:all=4.57.0-2 python3-traitlets:all=5.1.1-1 python3-tz:all=2021.3-1 python3-urllib3:all=1.26.5-1~exp1 python3-webencodings:all=0.5.1-4 python3-zipp:all=1.0.0-3 python3.9:amd64=3.9.7-4 python3.9-dev:amd64=3.9.7-4 python3.9-minimal:amd64=3.9.7-4 readline-common:all=8.1-2 rpcsvc-proto:amd64=1.4.2-4 sed:amd64=4.8-1 sensible-utils:all=0.0.17 sgml-base:all=1.30 sphinx-common:all=4.2.0-5 sysvinit-utils:amd64=3.00-1 tar:amd64=1.34+dfsg-1 ttf-bitstream-vera:all=1.10-8.1 tzdata:all=2021e-1 util-linux:amd64=2.37.2-4 xml-core:all=0.18+nmu1 xz-utils:amd64=5.2.5-2 zlib1g:amd64=1:1.2.11.dfsg-2 zlib1g-dev:amd64=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211104T150851Z/ unstable main
deb-src http://snapshot.notset.fr/archive/debian/20211104T150851Z/ unstable main
deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main
deb http://snapshot.notset.fr/archive/debian/20211014T155334Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d python-cogent=2021.10.12a1+dfsg-1 && mkdir -p /build/python-cogent-yPSVqR && dpkg-source --no-check -x /*.dsc /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg && chown -R builduser:builduser /build/python-cogent-yPSVqR" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1636014544" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/python-cogent-yPSVqR /tmp/python-cogent-2021.10.12a1+dfsg-1c54l8p6r bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm main
I: automatically chosen mode: root
I: chroot architecture amd64 is equal to the host's architecture
I: automatically chosen format: tar
I: using /tmp/mmdebstrap.PMfnIfpgYp as tempdir
I: running apt-get update...
I: downloading packages with apt...
I: extracting archives...
I: installing essential packages...
I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.PMfnIfpgYp
Reading package lists...
Building dependency tree...
util-linux is already the newest version (2.36.1-8).
The following NEW packages will be installed:
  fakeroot libfakeroot
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 134 kB of archives.
After this operation, 397 kB of additional disk space will be used.
Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB]
Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 134 kB in 0s (1036 kB/s)
Selecting previously unselected package libfakeroot:amd64.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 4668 files and directories currently installed.)
Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.25.3-1.1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ...
Unpacking fakeroot (1.25.3-1.1) ...
Setting up libfakeroot:amd64 (1.25.3-1.1) ...
Setting up fakeroot (1.25.3-1.1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Processing triggers for libc-bin (2.31-13) ...
I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/
I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211104T150851Z/ unstable main
deb-src http://snapshot.notset.fr/archive/debian/20211104T150851Z/ unstable main
deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main
deb http://snapshot.notset.fr/archive/debian/20211014T155334Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.PMfnIfpgYp
Get:1 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable InRelease [165 kB]
Hit:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease
Get:3 http://snapshot.notset.fr/archive/debian/20211014T155334Z unstable InRelease [165 kB]
Ign:4 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main Sources
Ign:5 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main amd64 Packages
Ign:4 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main Sources
Ign:5 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main amd64 Packages
Ign:4 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main Sources
Ign:5 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main amd64 Packages
Get:4 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main Sources [12.4 MB]
Get:5 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main amd64 Packages [11.9 MB]
Ign:6 http://snapshot.notset.fr/archive/debian/20211014T155334Z unstable/main amd64 Packages
Ign:6 http://snapshot.notset.fr/archive/debian/20211014T155334Z unstable/main amd64 Packages
Ign:6 http://snapshot.notset.fr/archive/debian/20211014T155334Z unstable/main amd64 Packages
Get:6 http://snapshot.notset.fr/archive/debian/20211014T155334Z unstable/main amd64 Packages [11.9 MB]
Fetched 36.5 MB in 30s (1211 kB/s)
Reading package lists...
I: installing remaining packages inside the chroot...
I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.PMfnIfpgYp
I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d python-cogent=2021.10.12a1+dfsg-1 && mkdir -p /build/python-cogent-yPSVqR && dpkg-source --no-check -x /*.dsc /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg && chown -R builduser:builduser /build/python-cogent-yPSVqR"' exec /tmp/mmdebstrap.PMfnIfpgYp
Reading package lists...
NOTICE: 'python-cogent' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-cogent.git
Please use:
git clone https://salsa.debian.org/med-team/python-cogent.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3027 kB of source archives.
Get:1 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main python-cogent 2021.10.12a1+dfsg-1 (dsc) [2572 B]
Get:2 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main python-cogent 2021.10.12a1+dfsg-1 (tar) [3013 kB]
Get:3 http://snapshot.notset.fr/archive/debian/20211104T150851Z unstable/main python-cogent 2021.10.12a1+dfsg-1 (diff) [11.6 kB]
Fetched 3027 kB in 2s (1238 kB/s)
Download complete and in download only mode
W: Download is performed unsandboxed as root as file 'python-cogent_2021.10.12a1+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)
dpkg-source: info: extracting python-cogent in /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg
dpkg-source: info: unpacking python-cogent_2021.10.12a1+dfsg.orig.tar.xz
dpkg-source: info: unpacking python-cogent_2021.10.12a1+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying sphinx.patch
dpkg-source: info: applying fix_interpreter.patch
I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1636014544" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.PMfnIfpgYp
dpkg-buildpackage: info: source package python-cogent
dpkg-buildpackage: info: source version 2021.10.12a1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
   dh_autoreconf_clean -O--buildsystem=pybuild
   debian/rules override_dh_clean
make[1]: Entering directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
#These files are rebuilt on-the-fly
for f in `find -name '*.c'` ; do \
    head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \
done
rm -rf build build-stamp
rm -rf doc/_build
dh_clean
make[1]: Leaving directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
 debian/rules binary-arch
dh binary-arch --with python3 --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
dh_auto_build
I: pybuild plugin_flit:66: Installing package /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/src/cogent3 -> /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3
I: pybuild plugin_flit:79: Writing dist-info /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/
set -x; cd doc; PYTHONPATH=/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg http_proxy='127.0.0.1:9' /usr/bin/make html
+ cd doc
+ PYTHONPATH=/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg http_proxy=127.0.0.1:9 /usr/bin/make html
make[2]: Entering directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc'
sphinx-build -b html -d _build/doctrees   . _build/html
Running Sphinx v4.2.0
making output directory... done
WARNING: html_static_path entry '_static' does not exist
WARNING: The config value `today' has type `date', defaults to `str'.
[autosummary] generating autosummary for: api/__init__/cogent3.__init__.available_apps.rst, api/__init__/cogent3.__init__.available_codes.rst, api/__init__/cogent3.__init__.available_models.rst, api/__init__/cogent3.__init__.available_moltypes.rst, api/__init__/cogent3.__init__.get_code.rst, api/__init__/cogent3.__init__.get_model.rst, api/__init__/cogent3.__init__.get_moltype.rst, api/__init__/cogent3.__init__.load_aligned_seqs.rst, api/__init__/cogent3.__init__.load_delimited.rst, api/__init__/cogent3.__init__.load_table.rst, ..., examples/scope_model_params_on_trees.rst, examples/seq_features.rst, examples/simple.rst, examples/simulate_alignment.rst, examples/testing_multi_loci.rst, general.rst, index.rst, install.rst, licenses.rst, pycogent.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 110 source files that are out of date
updating environment: [new config] 110 added, 0 changed, 0 removed
reading sources... [  0%] api/__init__/cogent3.__init__.available_apps
reading sources... [  1%] api/__init__/cogent3.__init__.available_codes
reading sources... [  2%] api/__init__/cogent3.__init__.available_models
reading sources... [  3%] api/__init__/cogent3.__init__.available_moltypes
reading sources... [  4%] api/__init__/cogent3.__init__.get_code
reading sources... [  5%] api/__init__/cogent3.__init__.get_model
reading sources... [  6%] api/__init__/cogent3.__init__.get_moltype
reading sources... [  7%] api/__init__/cogent3.__init__.load_aligned_seqs
reading sources... [  8%] api/__init__/cogent3.__init__.load_delimited
reading sources... [  9%] api/__init__/cogent3.__init__.load_table
reading sources... [ 10%] api/__init__/cogent3.__init__.load_tree
reading sources... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs
reading sources... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs
reading sources... [ 12%] api/__init__/cogent3.__init__.make_seq
reading sources... [ 13%] api/__init__/cogent3.__init__.make_table
reading sources... [ 14%] api/__init__/cogent3.__init__.make_tree
reading sources... [ 15%] api/__init__/cogent3.__init__.make_unaligned_seqs
reading sources... [ 16%] api/alignment/alignment
reading sources... [ 17%] api/alignment/classes/cogent3.core.alignment.Alignment
reading sources... [ 18%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment
reading sources... [ 19%] api/alignment/classes/cogent3.core.alignment.SequenceCollection
reading sources... [ 20%] api/alphabet/alphabet
reading sources... [ 20%] api/alphabet/classes/cogent3.core.alphabet.Alphabet
reading sources... [ 21%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode
reading sources... [ 22%] api/genetic_code/genetic_code
reading sources... [ 23%] api/index
reading sources... [ 24%] api/moltype/classes/cogent3.core.moltype.MolType
reading sources... [ 25%] api/moltype/moltype
reading sources... [ 26%] api/sequence/classes/cogent3.core.sequence.DnaSequence
reading sources... [ 27%] api/sequence/classes/cogent3.core.sequence.ProteinSequence
reading sources... [ 28%] api/sequence/classes/cogent3.core.sequence.RnaSequence
reading sources... [ 29%] api/sequence/sequence
reading sources... [ 30%] api/table/classes/cogent3.parse.table.FilteringParser
reading sources... [ 30%] api/table/classes/cogent3.util.table.Columns
reading sources... [ 31%] api/table/classes/cogent3.util.table.Table
reading sources... [ 32%] api/table/table
reading sources... [ 33%] api/tree/classes/cogent3.core.tree.PhyloNode
reading sources... [ 34%] api/tree/tree
reading sources... [ 35%] app/align-codon
reading sources... [ 36%] app/align-nucleotide
reading sources... [ 37%] app/align-protein
reading sources... [ 38%] app/app-overview
reading sources... [ 39%] app/available-apps
reading sources... [ 40%] app/dstore
reading sources... [ 40%] app/evo-ancestral-states
reading sources... [ 41%] app/evo-dt-nuc-model
reading sources... [ 42%] app/evo-extract-model-stats
reading sources... [ 43%] app/evo-hypothesis
reading sources... [ 44%] app/evo-model
reading sources... [ 45%] app/evo-model-timehet
reading sources... [ 46%] app/evo-model-with-tree
reading sources... [ 47%] app/evo-natsel_neutral
reading sources... [ 48%] app/evo-natsel_sitehet
reading sources... [ 49%] app/evo-natsel_timehet
reading sources... [ 50%] app/evo-natsel_zhang
reading sources... [ 50%] app/evo-nstat-codon-model
reading sources... [ 51%] app/evo-tr-codon-model
reading sources... [ 52%] app/evo-tr-nuc-model
reading sources... [ 53%] app/index
reading sources... [ 54%] app/not-completed
reading sources... [ 55%] app/user_function
reading sources... [ 56%] app/warning
reading sources... [ 57%] cookbook/DNA_and_RNA_sequences
reading sources... [ 58%] cookbook/alignments
reading sources... [ 59%] cookbook/alphabet
reading sources... [ 60%] cookbook/annotations
reading sources... [ 60%] cookbook/building_alignments
reading sources... [ 61%] cookbook/building_phylogenies
reading sources... [ 62%] cookbook/calc_genetic_distance
reading sources... [ 63%] cookbook/evo_modelling
reading sources... [ 64%] cookbook/genetic_code
reading sources... [ 65%] cookbook/index
reading sources... [ 66%] cookbook/loading_sequences
reading sources... [ 67%] cookbook/loading_tabular
reading sources... [ 68%] cookbook/manipulating_biological_data
reading sources... [ 69%] cookbook/moltypes
reading sources... [ 70%] cookbook/protein_sequences
reading sources... [ 70%] cookbook/simple_trees
reading sources... [ 71%] cookbook/tables
reading sources... [ 72%] cookbook/useful_utilities
reading sources... [ 73%] cookbook/what_codes
reading sources... [ 74%] data_file_links
reading sources... [ 75%] examples/align_codons_to_protein
reading sources... [ 76%] examples/calculate_UPGMA_cluster
reading sources... [ 77%] examples/calculate_neigbourjoining_tree
reading sources... [ 78%] examples/calculate_pairwise_distances
reading sources... [ 79%] examples/codon_models
reading sources... [ 80%] examples/coevolution
reading sources... [ 80%] examples/complete_seq_features
reading sources... [ 81%] examples/empirical_protein_models
reading sources... [ 82%] examples/hmm_par_heterogeneity
reading sources... [ 83%] examples/index
reading sources... [ 84%] examples/manipulating_tree_nodes
reading sources... [ 85%] examples/neutral_test
reading sources... [ 86%] examples/parallel
reading sources... [ 87%] examples/parametric_bootstrap
reading sources... [ 88%] examples/period_estimation
reading sources... [ 89%] examples/phylo_by_ls
reading sources... [ 90%] examples/rate_heterogeneity
reading sources... [ 90%] examples/relative_rate
reading sources... [ 91%] examples/scope_model_params_on_trees
reading sources... [ 92%] examples/seq_features
reading sources... [ 93%] examples/simple
reading sources... [ 94%] examples/simulate_alignment
reading sources... [ 95%] examples/testing_multi_loci
reading sources... [ 96%] general
reading sources... [ 97%] index
reading sources... [ 98%] install
reading sources... [ 99%] licenses
reading sources... [100%] pycogent

/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: WARNING: Unexpected section title.

Notes
-----
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.to_type:11: WARNING: Field list ends without a blank line; unexpected unindent.
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.entropy_per_seq:11: WARNING: Unexpected section title.

Notes
-----
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/../src/cogent3/core/alignment.py:docstring of cogent3.core.alignment.AlignmentI.to_type:11: WARNING: Field list ends without a blank line; unexpected unindent.
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io

    reader = io.load_unaligned(format="fasta")
    seqs = reader("data/SCA1-cds.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:23: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app.align import progressive_align

    codon_aligner = progressive_align("codon")
    aligned = codon_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:33: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aligned.info
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:46: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    nt_aligner = progressive_align("codon", distance="paralinear")
    aligned = nt_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:57: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)"
    codon_aligner = progressive_align("codon", guide_tree=tree)
    aligned = codon_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:67: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    codon_aligner = progressive_align(
        "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01
    )
    aligned = codon_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:80: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    codon_aligner = progressive_align(
        "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3)
    )
    aligned = codon_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:91: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aligned.info
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io

    reader = io.load_unaligned(format="fasta")
    seqs = reader("data/SCA1-cds.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:23: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app.align import progressive_align

    nt_aligner = progressive_align("nucleotide")
    aligned = nt_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    nt_aligner = progressive_align("nucleotide", distance="TN93")
    aligned = nt_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:45: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)"
    nt_aligner = progressive_align("nucleotide", guide_tree=tree)
    aligned = nt_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:59: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)"
    nt_aligner = progressive_align("F81", guide_tree=tree)
    aligned = nt_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:69: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aligned.info
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, translate

    reader = io.load_unaligned(format="fasta")
    to_aa = translate.translate_seqs()
    process = reader + to_aa
    seqs = process("data/SCA1-cds.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:25: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app.align import progressive_align

    aa_aligner = progressive_align("protein")
    aligned = aa_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:40: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aa_aligner = progressive_align("protein", distance="paralinear")
    aligned = aa_aligner(seqs)
    aligned
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:49: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aligned.info
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/available-apps.rst:8: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import available_apps

    available_apps()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:24: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app.io import get_data_store

    dstore = get_data_store("data/raw.zip", suffix="fa*", limit=5)
    dstore
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    m = dstore[0]
    m
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:41: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    m.read()[:20]  # truncating
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:50: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dstore.tail()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:57: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dstore.filtered("*ENSG00000067704*")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:64: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    for m in dstore:
        print(m)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:85: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dstore = get_data_store("data/demo-locked.tinydb")
    dstore.describe
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:92: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dstore.unlock(force=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:101: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dstore.summary_logs
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:107: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dstore.logs
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:113: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(dstore.logs[0].read()[:225])  # truncated for clarity
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    reader = io.load_aligned(format="fasta")
    aln = reader("data/primate_brca1.fasta")
    gn = evo.model("GN", tree="data/primate_brca1.tree")
    result = gn(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:25: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    reconstuctor = evo.ancestral_states()
    states_result = reconstuctor(result)
    states_result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:33: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    states_result["edge.0"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-ancestral-states.rst:39: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.tree.get_figure(contemporaneous=True).show(width=500, height=500)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")
    model = evo.model("BH", tree="data/primate_brca1.tree")
    result = model(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:27: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tree = result.tree
    fig = tree.get_figure()
    fig.scale_bar = "top right"
    fig.show(width=500, height=500)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tabulator = evo.tabulate_stats()
    stats = tabulator(result)
    stats
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:54: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    stats["edge motif motif2 params"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")
    model = evo.model("GN", tree="data/primate_brca1.tree")
    result = model(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:25: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tabulator = evo.tabulate_stats()
    tabulated = tabulator(result)
    tabulated
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:38: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tabulated["edge params"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:49: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tabulated["global params"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-extract-model-stats.rst:58: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tabulated["motif params"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo, sample

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:18: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tree = "data/primate_brca1.tree"
    sm_args = dict(optimise_motif_probs=True)

    null = evo.model("GTR", tree=tree, sm_args=sm_args)
    alt = evo.model("GN", tree=tree, sm_args=sm_args)
    hyp = evo.hypothesis(null, alt)
    result = hyp(aln)
    type(result)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:31: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:43: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.LR, result.df, result.pvalue
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:52: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.null
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:56: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.null.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:63: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.alt.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:12: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, sample

    reader = io.load_aligned(format="fasta", moltype="dna")
    select_seqs = sample.take_named_seqs("Human", "Rhesus", "Galago")
    process = reader + select_seqs
    aln = process("data/primate_brca1.fasta")
    aln.names
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:26: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import evo

    gn = evo.model("GN")
    gn
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:35: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted = gn(aln)
    type(fitted)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:49: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:55: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:59: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted.lnL, fitted.nfp
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:63: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted.source
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:69: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted.tree, fitted.alignment
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:75: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted.total_length(length_as="paralinear")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:84: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    gn = evo.model("GN", split_codons=True)

    fitted = gn(aln)
    fitted
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:95: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted[3]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.app import io, evo

    tree = load_tree("data/primate_brca1.tree")
    fig = tree.get_figure(contemporaneous=True)
    fig.style_edges(
        "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red")
    )
    fig.show(width=500, height=500)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:32: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    time_het = evo.model(
        "GN",
        tree=tree,
        time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")],
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:42: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    reader = io.load_aligned(format="fasta")
    aln = reader("data/primate_brca1.fasta")
    result = time_het(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:50: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io

    reader = io.load_aligned(format="fasta", moltype="dna")
    aln = reader("data/primate_brca1.fasta")
    aln.names
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:22: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.app import evo

    tree = load_tree("data/primate_brca1.tree")
    gn = evo.model("GN", tree=tree)
    gn
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    gn = evo.model("GN", tree="data/primate_brca1.tree")
    gn
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:42: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted = gn(aln)
    fitted
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:51: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    fitted.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")

    omega_eq_1 = evo.natsel_neutral(
        "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False
    )
    result = omega_eq_1(aln)
    type(result)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:26: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:30: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.alt.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")

    sites_differ = evo.natsel_sitehet(
        "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False
    )

    result = sites_differ(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:29: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.alt.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:38: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    bprobs = result.alt.lf.get_bin_probs()
    bprobs[:, :20]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_timehet.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_timehet.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")

    hc_differ = evo.natsel_timehet(
        "GNC",
        tree="data/primate_brca1.tree",
        optimise_motif_probs=False,
        tip1="Human",
        tip2="Chimpanzee",
    )
    result = hc_differ(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_timehet.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.alt.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    from numpy import array
    from cogent3 import make_table
    from IPython.core.display import HTML

    header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges']
    data = {'Site Class': array(['0', '1', '2a', '2b'], dtype='<U2'), 'Proportion': array(['p0', 'p1', 'p2', 'p3'], dtype='<U2'), 'Background Edges': array(['0 < omega0 < 1', 'omega1 = 1', '0 < omega0 < 1', 'omega1 = 1'],
      dtype='<U14'), 'Foreground Edges': array(['0 < omega0 < 1', 'omega1 = 1', '0 < omega2 > 1', '0 < omega0 < 1'],
      dtype='<U14')}
    data = {k: array(data[k], dtype='U') for k in data}
    table = make_table(header, data=data)
    HTML(table.set_repr_policy(show_shape=False))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:30: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")

    zhang_test = evo.natsel_zhang(
        "GNC",
        tree="data/primate_brca1.tree",
        optimise_motif_probs=False,
        tip1="Human",
        tip2="Chimpanzee",
    )

    result = zhang_test(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.alt.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:55: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    bprobs = result.alt.lf.get_bin_probs()
    bprobs[:, :20]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:63: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tab = evo.tabulate_stats()
    stats = tab(result.alt)
    stats
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:69: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    stats["edge bin params"][:10]  # truncating the table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-nstat-codon-model.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-nstat-codon-model.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-nstat-codon-model.rst:22: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    model = evo.model("GNC", tree="data/primate_brca1.tree")
    result = model(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-nstat-codon-model.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-nstat-codon-model.rst:37: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tree = result.tree
    fig = tree.get_figure()
    fig.scale_bar = "top right"
    fig.show(width=500, height=500)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-codon-model.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-codon-model.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import available_models

    available_models("codon")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-codon-model.rst:22: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")
    model = evo.model(
        "CNFGTR",
        tree="data/primate_brca1.tree",
        sm_args=dict(optimise_motif_probs=True),
    )
    result = model(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-codon-model.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-nuc-model.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-nuc-model.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import available_models

    available_models("nucleotide")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-nuc-model.rst:22: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, evo

    loader = io.load_aligned(format="fasta", moltype="dna")
    aln = loader("data/primate_brca1.fasta")
    model = evo.model(
        "GTR", tree="data/primate_brca1.tree", sm_args=dict(optimise_motif_probs=True)
    )
    result = model(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-nuc-model.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result.lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/not-completed.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/not-completed.rst:24: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app import io, sample

    reader = io.load_aligned(format="fasta")
    select_seqs = sample.take_named_seqs("Mouse", "Human")
    aln = reader("data/primate_brca1.fasta")
    result = select_seqs(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/not-completed.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    result == False
    result.type
    result.message
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/not-completed.rst:45: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises:

    result = reader("primate_brca1.fasta")
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/not-completed.rst:54: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    process = reader + select_seqs
    result = process("data/primate_brca1.fasta")
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/not-completed.rst:62: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises:

    result = process("primate_brca1.fasta")
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/user_function.rst:25: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app.composable import ALIGNED_TYPE, appify

    @appify(ALIGNED_TYPE, ALIGNED_TYPE, data_types="Alignment")
    def up_to(val, index=4):
        return val[:index]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/user_function.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    up_to
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/user_function.rst:42: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    first4 = up_to(index=4)
    first4
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/user_function.rst:49: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna"
    )
    result = first4(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/user_function.rst:66: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app.composable import (
        ALIGNED_TYPE,
        SEQUENCE_TYPE,
        SERIALISABLE_TYPE,
        appify,
    )

    @appify((ALIGNED_TYPE, SEQUENCE_TYPE), SERIALISABLE_TYPE)
    def rename_seqs(aln):
        """upper case names"""
        return aln.rename_seqs(lambda x: x.upper())

    renamer = rename_seqs()
    result = renamer(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/app/user_function.rst:89: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.app.composable import (
        ALIGNED_TYPE,
        PAIRWISE_DISTANCE_TYPE,
        appify,
    )

    @appify(ALIGNED_TYPE, PAIRWISE_DISTANCE_TYPE)
    def get_dists(aln, calc="hamming"):
        return aln.distance_matrix(calc=calc, show_progress=False)

    percent_dist = get_dists(calc="percent")
    result = percent_dist(aln)
    result
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:20: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    my_seq = DNA.make_seq("AGTACACTGGT")
    my_seq
    print(my_seq)
    str(my_seq)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:32: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import RNA

    rnaseq = RNA.make_seq("ACGUACGUACGUACGU")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:41: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    my_seq = DNA.make_seq("AGTACACTGGT")
    print(my_seq.to_fasta())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:51: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import RNA

    rnaseq = RNA.make_seq("ACGUACGUACGUACGU")
    rnaseq.to_fasta()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:63: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq

    my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna")
    my_seq
    type(my_seq)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:74: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq

    my_seq = make_seq("AGTACACTGGT", moltype="dna")
    my_seq.name = "my_gene"
    print(my_seq.to_fasta())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:85: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    my_seq = DNA.make_seq("AGTACACTGGT")
    print(my_seq.complement())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:95: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(my_seq.rc())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:101: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(my_seq.rc())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:110: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    my_seq = DNA.make_seq("GCTTGGGAAAGTCAAATGGAA", "protein-X")
    pep = my_seq.get_translation()
    type(pep)
    print(pep.to_fasta())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:122: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    my_seq = DNA.make_seq("ACGTACGTACGTACGT")
    print(my_seq.to_rna())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:132: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import RNA

    rnaseq = RNA.make_seq("ACGUACGUACGUACGU")
    print(rnaseq.to_dna())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:142: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    a = DNA.make_seq("AGTACACTGGT")
    a.can_pair(a.complement())
    a.can_pair(a.rc())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:153: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    my_seq = DNA.make_seq("AGTACACTGGT")
    extra_seq = DNA.make_seq("CTGAC")
    long_seq = my_seq + extra_seq
    long_seq
    str(long_seq)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:166: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    my_seq[1:6]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:177: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    seq = DNA.make_array_seq("ATGATGATGATG")
    pos3 = seq[2::3]
    assert str(pos3) == "GGGG"
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:190: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    seq = DNA.make_seq("ATGATGATGATG")
    indices = [(i, i + 2) for i in range(len(seq))[::3]]
    pos12 = seq.add_feature("pos12", "pos12", indices)
    pos12 = pos12.get_slice()
    assert str(pos12) == "ATATATAT"
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:211: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import RNA

    s = RNA.make_seq("--AUUAUGCUAU-UAu--")
    print(s.degap())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs, make_unaligned_seqs

    dna = {"seq1": "ATGACC", "seq2": "ATCGCC"}
    seqs = make_aligned_seqs(data=dna, moltype="dna")
    print(type(seqs))
    seqs = make_unaligned_seqs(dna, moltype="dna")
    print(type(seqs))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:41: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    dna = {"seq1": "ATGACC", "seq2": "ATCGCC"}
    seqs = make_aligned_seqs(data=dna, moltype="dna", array_align=True)
    print(type(seqs))
    print(seqs)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_unaligned_seqs

    seqs = load_unaligned_seqs("data/test.paml")
    print(seqs)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:70: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")],
        moltype="dna",
    )
    print(aln)
    new_seqs = make_aligned_seqs(
        [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna"
    )
    new_aln = aln.add_seqs(new_seqs)
    print(new_aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:92: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    new_aln = aln.add_seqs(new_seqs, before_name="seq2")
    print(new_aln)
    new_aln = aln.add_seqs(new_seqs, after_name="seq2")
    print(new_aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:104: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")],
        moltype="dna",
    )
    ref_aln = make_aligned_seqs(
        [("seq3", "ATAGGATG"), ("seq0", "ATG-AGCG"), ("seq4", "ATGCTGGG")],
        moltype="dna",
    )
    new_aln = aln.add_from_ref_aln(ref_aln)
    print(new_aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:126: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        [("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")],
        moltype="dna",
    )
    new_aln = aln.get_degapped_relative_to("seq1")
    print(new_aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:145: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")],
        moltype="dna",
        array_align=False,
    )
    seq = aln.get_seq("seq1")
    seq.name
    type(seq)
    seq.is_gapped()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:161: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seq = aln.get_gapped_seq("seq1")
    seq.is_gapped()
    print(seq)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:169: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln.names
    aln.names
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:179: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_unaligned_seqs, load_aligned_seqs

    fn = "data/long_testseqs.fasta"
    seqs = load_unaligned_seqs(fn, moltype="dna")
    my_seq = seqs.seqs[0]
    my_seq[:24]
    str(my_seq[:24])
    type(my_seq)
    aln = load_aligned_seqs(fn, moltype="dna")
    aln.seqs[0][:24]
    print(aln.seqs[0][:24])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:196: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/test.paml", moltype="dna")
    aln.names
    new = aln.take_seqs(["Human", "HowlerMon"])
    new.names
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:207: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/test.paml", array_align=False, moltype="dna")
    seq = aln.get_seq("Human")
    new = aln.take_seqs(["Human", "HowlerMon"])
    id(new.get_seq("Human")) == id(aln.get_seq("Human"))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:222: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_unaligned_seqs
    from cogent3.core.alignment import Alignment

    seq = load_unaligned_seqs("data/test.paml")
    aln = Alignment(seq)
    fasta_1 = seq
    fasta_2 = aln
    assert fasta_1 == fasta_2
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:238: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    data = [("a", "ACG---"), ("b", "CCTGGG")]
    aln = make_aligned_seqs(data=data)
    dna = aln.to_dna()
    dna
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:249: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    data = [("a", "ACG---"), ("b", "CCUGGG")]
    aln = make_aligned_seqs(data=data)
    rna = aln.to_rna()
    rna
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:260: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    data = [("x", "TYV"), ("y", "TE-")]
    aln = make_aligned_seqs(data=data)
    prot = aln.to_protein()
    prot
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:277: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
    degapped = aln.degap()
    print(type(degapped))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:292: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    dna = {"seq1": "ATGACC", "seq2": "ATCGCC"}
    aln = make_aligned_seqs(data=dna, moltype="dna")
    aln.write("sample.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:302: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln.write("sample", format="fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:308: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import remove_files

    remove_files(["sample", "sample.fasta"], error_on_missing=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:317: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs
    from cogent3.core.alignment import Alignment

    seq = load_aligned_seqs("data/long_testseqs.fasta")
    aln = Alignment(seq)
    fasta_align = aln
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:329: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs
    from cogent3.core.alignment import Alignment

    seq = load_aligned_seqs("data/test.paml")
    aln = Alignment(seq)
    got = aln.to_phylip()
    print(got)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:342: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs
    from cogent3.core.alignment import Alignment

    seq = load_aligned_seqs("data/test.paml")
    aln = Alignment(seq)
    string_list = aln.to_dict().values()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:359: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    fn = "data/long_testseqs.fasta"
    aln = load_aligned_seqs(fn, moltype="dna")
    print(aln[:24])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:369: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: TypeError

    from cogent3 import load_unaligned_seqs

    fn = "data/long_testseqs.fasta"
    seqs = load_unaligned_seqs(fn)
    print(seqs[:24])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:381: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    seq = load_aligned_seqs("data/test.paml")
    column_four = aln[3]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:391: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    region = aln[50:70]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:401: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
    col = aln[113:115].iter_positions()
    type(col)
    list(col)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:415: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=False
    )
    list(range(len(aln))[2::3])
    indices = [(i, i + 1) for i in range(len(aln))[2::3]]
    indices
    pos3 = aln.add_feature("pos3", "pos3", indices)
    pos3 = pos3.get_slice()
    print(pos3)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:434: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=True
    )
    pos3 = aln[2::3]
    print(pos3)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:454: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"},
        moltype="dna",
    )
    new = aln.trim_stop_codons()
    print(new)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:467: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        data={
            "seq1": "ACGTAA---",
            "seq2": "ACGAC----",  # terminal codon incomplete
            "seq3": "ACGCAATGA",
        },
        moltype="dna",
    )
    new = aln.trim_stop_codons(allow_partial=True)
    print(new)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:485: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data=[
            ("seq1", "ATGAAGGTG---"),
            ("seq2", "ATGAAGGTGATG"),
            ("seq3", "ATGAAGGNGATG"),
        ],
        moltype="dna",
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:500: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    nucs = aln.no_degenerates()
    print(nucs)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:507: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    trinucs = aln.no_degenerates(motif_length=3)
    print(trinucs)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:515: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    pos = aln.variable_positions()
    just_variable_aln = aln.take_positions(pos)
    print(just_variable_aln[:10])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:527: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    pos = aln.variable_positions()
    just_constant_aln = aln.take_positions(pos, negate=True)
    print(just_constant_aln[:10])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:541: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    variable_codons = aln.filtered(
        lambda x: len(set(map(tuple, x))) > 1, motif_length=3
    )
    print(just_variable_aln[:9])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:553: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = aln.to_type(array_align=False)
    variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3)
    print(just_variable_aln[:9])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:567: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    aln.take_seqs(["Human", "Mouse"])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:576: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln.take_seqs(["Human", "Mouse"], negate=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:585: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data=[
            ("seq1", "ATGAAGGTG---"),
            ("seq2", "ATGAAGGTGATG"),
            ("seq3", "ATGAAGGNGATG"),
        ],
        moltype="dna",
    )

    def no_N_chars(s):
        return "N" not in s

    aln.take_seqs_if(no_N_chars)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:605: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln.take_seqs_if(no_N_chars, negate=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:617: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data=[
            ("seq1", "ATGAAGGTG---"),
            ("seq2", "ATGAAGGTGATG"),
            ("seq3", "ATGAAGGNGATG"),
        ],
        moltype="dna",
    )
    counts = aln.counts()
    print(counts)
    counts = aln.counts(motif_length=3)
    print(counts)
    counts = aln.counts(include_ambiguity=True)
    print(counts)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:645: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna")
    motif_probs = aln.get_motif_probs()
    print(motif_probs)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:655: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, DNA

    trinuc_alphabet = DNA.alphabet.get_word_alphabet(3)
    aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna")
    motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet)
    for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True):
        print("%s  %.3f" % (m, motif_probs[m]))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:669: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna")
    motif_probs = aln.get_motif_probs()
    assert motif_probs["T"] == 0.0
    motif_probs = aln.get_motif_probs(pseudocount=1e-6)
    assert 0 < motif_probs["T"] <= 1e-6
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:681: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")]
    aln = make_aligned_seqs(data=seqs, moltype="dna")
    dinuc_alphabet = DNA.alphabet.get_word_alphabet(2)
    motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet)
    assert motif_probs["AA"] == 0.25
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:691: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seqs = [("my_seq", "AAAGTAAG")]
    aln = make_aligned_seqs(data=seqs, moltype="dna")
    my_seq = aln.get_seq("my_seq")
    my_seq.count("AA")
    "AAA".count("AA")
    "AAAA".count("AA")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:702: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq

    seq = make_seq(moltype="dna", seq="AAAGTAAG")
    seq
    di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)]
    sum([nn == "AA" for nn in di_nucs])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:717: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
    col = aln[113:115].iter_positions()
    c1, c2 = list(col)
    c1, c2
    list(filter(lambda x: x == "-", c1))
    list(filter(lambda x: x == "-", c2))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:731: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
    for column in aln[113:150].iter_positions():
        ungapped = list(filter(lambda x: x == "-", column))
        gap_fraction = len(ungapped) * 1.0 / len(column)
        print(gap_fraction)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:746: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data=[
            ("seq1", "ATGAAGG-TG--"),
            ("seq2", "ATG-AGGTGATG"),
            ("seq3", "ATGAAG--GATG"),
        ],
        moltype="dna",
    )
    seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:762: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seq_to_aln_map[3]
    seq_to_aln_map[8]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:771: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1]
    aln_to_seq_map[3]
    aln_to_seq_map[8]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:779: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: KeyError

    seq_pos = aln_to_seq_map[7]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:793: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        data=[
            ("seq1", "ATGAA---TG-"),
            ("seq2", "ATG-AGTGATG"),
            ("seq3", "AT--AG-GATG"),
        ],
        moltype="dna",
    )
    print(aln.omit_gap_runs(2))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:807: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        data=[
            ("seq1", "ATGAA---TG-"),
            ("seq2", "ATG-AGTGATG"),
            ("seq3", "AT--AG-GATG"),
        ],
        moltype="dna",
    )
    print(aln.omit_gap_pos(0.40))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:821: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        data=[
            ("seq1", "ATGAA------"),
            ("seq2", "ATG-AGTGATG"),
            ("seq3", "AT--AG-GATG"),
        ],
        moltype="dna",
    )
    filtered_aln = aln.omit_gap_seqs(0.50)
    print(filtered_aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:836: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(filtered_aln.omit_gap_pos())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA, PROTEIN

    print(DNA.alphabet)
    print(PROTEIN.alphabet)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:20: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    PROTEIN.alphabet.moltype == PROTEIN
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:29: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dinuc_alphabet = DNA.alphabet.get_word_alphabet(2)
    print(dinuc_alphabet)
    trinuc_alphabet = DNA.alphabet.get_word_alphabet(3)
    print(trinuc_alphabet)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:39: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seq = "TAGT"
    indices = DNA.alphabet.to_indices(seq)
    indices
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seq = DNA.alphabet.from_indices([0, 2, 3, 0])
    seq
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:55: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seq = DNA.alphabet.from_ordinals_to_seq([0, 2, 3, 0])
    seq
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:21: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.genbank import RichGenbankParser

    parser = RichGenbankParser(open("data/ST_genome_part.gb"))
    for accession, seq in parser:
        print(accession)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:29: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    cds = seq.get_annotations_matching("CDS")
    print(cds)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:39: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.core.annotation import Feature

    def add_annotation(seq, feature, spans):
        type_ = feature["type"]
        if type_ != "CDS":
            return
        name = feature.get("locus_tag", None)
        if name and not isinstance(name, str):
            name = " ".join(name)
        seq.add_annotation(Feature, type_, name, spans)

    parser = RichGenbankParser(
        open("data/ST_genome_part.gb"), add_annotation=add_annotation
    )
    for accession, seq in parser:  # just reading one accession,sequence
        break
    genes = seq.get_annotations_matching("CDS")
    print(genes)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:63: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA
    from cogent3.core.annotation import Feature

    s1 = DNA.make_seq(
        "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
    )
    print(s1[10:15])  # this will be exon 1
    print(s1[30:40])  # this will be exon 2
    print(s1[45:48])  # this will be exon 3
    s2 = DNA.make_seq("CGAAACGTTT", name="seq2")
    s3 = DNA.make_seq("CGAAACGTTT", name="seq3")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:83: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA
    from cogent3.core.annotation import Feature

    s1 = DNA.make_seq(
        "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
    )
    exon1 = s1.add_annotation(Feature, "exon", "A", [(10, 15)])
    exon2 = s1.add_annotation(Feature, "exon", "B", [(30, 40)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:97: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    s1 = DNA.make_seq(
        "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
    )
    exon3 = s1.add_feature("exon", "C", [(45, 48)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:111: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    s2 = DNA.make_seq("CGAAACGTTT", name="seq2")
    cpgs_series = s2.add_feature("cpgsite", "cpg", [(0, 2), (5, 7)])
    s3 = DNA.make_seq("CGAAACGTTT", name="seq3")
    cpg1 = s3.add_feature("cpgsite", "cpg", [(0, 2)])
    cpg2 = s3.add_feature("cpgsite", "cpg", [(5, 7)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:126: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    s1 = DNA.make_seq(
        "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
    )
    exon1 = s1.add_feature("exon", "A", [(10, 15)])
    exon2 = s1.add_feature("exon", "B", [(30, 40)])
    exon3 = s1.add_feature("exon", "C", [(45, 48)])
    cds = s1.get_region_covering_all([exon1, exon2, exon3])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:143: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    cds.get_coordinates()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:152: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    not_cds = cds.get_shadow()
    not_cds
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:159: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    cds
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:168: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln1 = make_aligned_seqs(
        data=[["x", "-AAACCCCCA"], ["y", "TTTT--TTTT"]], array_align=False
    )
    seq_exon = aln1.get_seq("x").add_feature("exon", "A", [(3, 8)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:182: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.core.annotation import Variable

    red_data = aln1.add_annotation(
        Variable, "redline", "align", [((0, 15), 1), ((15, 30), 2), ((30, 45), 3)]
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:195: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    s1 = DNA.make_seq(
        "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
    )
    exon1 = s1.add_feature("exon", "A", [(10, 15)])
    exon2 = s1.add_feature("exon", "B", [(30, 40)])
    s1[exon1]
    s1[10:15]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:209: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    s1[exon2]
    exon2.get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:217: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    s1 = DNA.make_seq(
        "AAGAAGAAGACCCCCAAAAAAAAAA" "TTTTTTTTTTAAAAAGGGAACCCT", name="seq1"
    )
    exon1 = s1.add_feature("exon", "A", [(10, 15)])
    exon2 = s1.add_feature("exon", "B", [(30, 40)])
    exon3 = s1.add_feature("exon", "C", [(45, 48)])
    cds = s1.get_region_covering_all([exon1, exon2, exon3])
    print(s1[cds])
    print(s1[exon1, exon2, exon3])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:233: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(s1)
    print(s1[exon1, exon2, exon3])
    print(s1[exon2])
    print(s1[exon3])
    print(s1[exon1, exon3, exon2])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:244: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: ValueError

    s1[1:10, 9:15]
    s1[exon1, exon1]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:252: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(s1.get_region_covering_all([exon3, exon3]).get_slice())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:259: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(s1[exon2])
    ex2_start = exon2[0:3]
    print(s1[ex2_start])
    ex2_end = exon2[-3:]
    print(s1[ex2_end])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:272: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: ValueError

    aln1[seq_exon]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:282: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln2 = make_aligned_seqs(
        data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
    )
    seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
    match_exon = seq.add_feature("exon", "A", [(3, 8)])
    aln2.get_seq("x").copy_annotations(seq)
    copied = list(aln2.get_annotations_from_seq("x", "exon"))
    copied
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:295: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln2 = make_aligned_seqs(data=[["x", "-AAAA"], ["y", "TTTTT"]], array_align=False)
    seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
    match_exon = seq.add_feature("exon", "A", [(5, 8)])
    aln2.get_seq("x").copy_annotations(seq)
    copied = list(aln2.get_annotations_from_seq("x", "exon"))
    copied
    copied[0].get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:307: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    # new test
    aln2 = make_aligned_seqs(
        data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
    )
    seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
    match_exon = seq.add_feature("exon", "A", [(5, 8)])
    aln2.get_seq("y").copy_annotations(seq)
    copied = list(aln2.get_annotations_from_seq("y", "exon"))
    copied
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:321: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln2 = make_aligned_seqs(
        data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
    )
    diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x")
    nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)])
    aln2.get_seq("y").copy_annotations(diff_len_seq)
    copied = list(aln2.get_annotations_from_seq("y", "repeat"))
    copied
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:337: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln_exon = aln1.get_annotations_from_any_seq("exon")
    print(aln1[aln_exon])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:345: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: ValueError

    cpgsite2 = s2.get_annotations_matching("cpgsite")
    print(s2[cpgsite2])
    cpgsite3 = s3.get_annotations_matching("cpgsite")
    s2[cpgsite3]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:358: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    # this test is new
    dont_exist = s2.get_annotations_matching("dont_exist")
    dont_exist
    s2[dont_exist]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:370: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln3 = make_aligned_seqs(
        data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False
    )
    exon = aln3.get_seq("x").add_feature("exon", "ex1", [(0, 4)])
    print(exon.get_slice())
    aln_exons = list(aln3.get_annotations_from_seq("x", "exon"))
    print(aln_exons)
    print(aln3[aln_exons])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:388: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    unified = aln_exons[0].as_one_span()
    print(aln3[unified])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:398: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    plus = DNA.make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG")
    plus_rpt = plus.add_feature("blah", "a", [(5, 15), (25, 28)])
    print(plus[plus_rpt])
    minus = plus.rc()
    print(minus)
    minus_rpt = minus.get_annotations_matching("blah")
    print(minus[minus_rpt])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:413: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.genbank import RichGenbankParser

    parser = RichGenbankParser(open("data/ST_genome_part.gb"))
    seq = [seq for accession, seq in parser][0]
    no_cds = seq.with_masked_annotations("CDS")
    print(no_cds[150:400])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:429: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]],
        moltype="dna",
        array_align=False,
    )
    exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)])
    print(aln.with_masked_annotations("exon", mask_char="?"))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:443: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rc = aln.rc()
    print(rc)
    print(rc.with_masked_annotations("exon", mask_char="?"))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:452: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    s = DNA.make_seq("CCCCAAAAAGGGAA", "x")
    exon = s.add_feature("exon", "norwegian", [(0, 4)])
    rpt = s.add_feature("repeat", "norwegian", [(9, 12)])
    rc = s.rc()
    print(s.with_masked_annotations("exon", shadow=True))
    print(rc.with_masked_annotations("exon", shadow=True))
    print(s.with_masked_annotations(["exon", "repeat"], shadow=True))
    print(rc.with_masked_annotations(["exon", "repeat"], shadow=True))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:468: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    s = DNA.make_seq("ATGACCCTGTAAAAAATGTGTTAACCC", name="a")
    cds1 = s.add_feature("cds", "cds1", [(0, 12)])
    cds2 = s.add_feature("cds", "cds2", [(15, 24)])
    all_cds = s.get_annotations_matching("cds")
    all_cds
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:483: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.genbank import RichGenbankParser

    parser = RichGenbankParser(open("data/ST_genome_part.gb"))
    seq = [seq for accession, seq in parser][0]
    all_cds = seq.get_annotations_matching("CDS")
    coding_seqs = seq.get_region_covering_all(all_cds)
    coding_seqs
    coding_seqs.get_slice()
    noncoding_seqs = coding_seqs.get_shadow()
    noncoding_seqs
    noncoding_seqs.get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:502: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
    )
    print(aln)
    exon = aln.get_seq("x").add_feature("exon", "1", [(3, 8)])
    aln_exons = aln.get_annotations_from_seq("x", "exon")
    aln_exons = aln.get_annotations_from_any_seq("exon")
    aln_exons
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:522: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    seq = DNA.make_seq("aaaccggttt" * 10)
    v = seq.add_feature("exon", "exon", [(20, 35)])
    v = seq.add_feature("repeat_unit", "repeat_unit", [(39, 49)])
    v = seq.add_feature("repeat_unit", "rep2", [(49, 60)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:536: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    from cogent3.util.misc import remove_files

    remove_files(["annotated_%d.png" % i for i in range(1, 4)], error_on_missing=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:17: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_unaligned_seqs, make_tree
    from cogent3.align.progressive import TreeAlign
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:24: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna")
    aln, tree = TreeAlign("HKY85", seqs, show_progress=False)
    aln
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:32: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tree = make_tree(
        "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)"
    )
    params = {"kappa": 4.0}
    aln, tree = TreeAlign(
        "HKY85", seqs, tree=tree, param_vals=params, show_progress=False
    )
    aln
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_unaligned_seqs, make_tree
    from cogent3.align.progressive import TreeAlign

    seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna")
    tree = make_tree(
        "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)"
    )
    params = {"kappa": 4.0, "omega": 1.3}
    aln, tree = TreeAlign(
        "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False
    )
    aln
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:68: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_unaligned_seqs
    from cogent3.evolve.models import get_model
    from cogent3.align.progressive import TreeAlign

    seqs = [
        (
            "hum",
            "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT",
        ),
        (
            "mus",
            "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG",
        ),
        ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"),
    ]
    unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna")
    print(unaligned_DNA)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:88: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(unaligned_DNA.get_translation())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:94: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aligned_aa_seqs = [
        ("hum", "KQIQESSENGSLAARQERQAQVNLT"),
        ("mus", "KQIQESGESGSLAARQERQAQVNLT"),
        ("rat", "LNKQ------PLS---------NKK"),
    ]
    aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_alignments.rst:107: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True)
    aligned_DNA
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:18: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
    tree = aln.quick_tree(calc="TN93", show_progress=False)
    tree = tree.balanced()  # purely for display
    print(tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:29: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
    dists = aln.distance_matrix(calc="TN93")
    tree = dists.quick_tree(show_progress=False)
    tree = tree.balanced()  # purely for display
    print(tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:49: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.phylo import nj
    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
    dists = aln.distance_matrix(calc="TN93")
    tree = nj.nj(dists, show_progress=False)
    tree = tree.balanced()  # purely for display
    print(tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:63: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.phylo import nj

    dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73}
    tree = nj.nj(dists, show_progress=False)
    print(tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:76: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.deserialise import deserialise_object
    from cogent3.phylo.least_squares import WLS

    dists = deserialise_object("data/dists_for_phylo.json")
    ls = WLS(dists)
    stat, tree = ls.trex(a=5, k=5, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/building_phylogenies.rst:92: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs
    from cogent3.phylo.maximum_likelihood import ML
    from cogent3.evolve.models import F81

    aln = load_aligned_seqs("data/primate_brca1.fasta")
    ml = ML(F81(), aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:16: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import available_distances

    available_distances()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:27: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
    dists = aln.distance_matrix(calc="tn93", show_progress=False)
    dists
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:38: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, get_distance_calculator

    aln = load_aligned_seqs("data/primate_brca1.fasta")
    dist_calc = get_distance_calculator("tn93", alignment=aln)
    dist_calc
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:46: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dist_calc.run(show_progress=False)
    dists = dist_calc.get_pairwise_distances()
    dists
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:54: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dist_calc.stderr
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:65: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, get_model
    from cogent3.evolve import distance

    aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
    d = distance.EstimateDistances(aln, submodel=get_model("F81"))
    d.run(show_progress=False)
    dists = d.get_pairwise_distances()
    dists
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:18: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import available_models

    available_models()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:27: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import get_model

    hky = get_model("HKY85")
    print(hky)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:44: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import get_model

    sub_mod = get_model("GTR", with_rate=True, distribution="gamma")
    print(sub_mod)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:56: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import get_model

    sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma")
    print(sub_mod)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:68: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import get_model

    sub_mod = get_model("JTT92", with_rate=True, distribution="gamma")
    print(sub_mod)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:80: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_tree
    from cogent3.evolve.models import get_model

    sub_mod = get_model("F81")
    tree = make_tree("(a,b,(c,d))")
    lf = sub_mod.make_likelihood_function(tree)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:94: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_tree, make_aligned_seqs
    from cogent3.evolve.models import get_model

    sub_mod = get_model("F81")
    tree = make_tree("(a,b,(c,d))")
    lf = sub_mod.make_likelihood_function(tree)
    aln = make_aligned_seqs(
        [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")]
    )
    lf.set_alignment(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:112: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    print(tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:120: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    sm = get_model("CNFGTR")
    lf = sm.make_likelihood_function(tree, digits=2)
    lf.set_param_rule(
        "omega",
        tip_names=["Human", "Orangutan"],
        outgroup_name="Galago",
        clade=True,
        init=0.5,
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:134: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:145: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    sm = get_model("CNFGTR")
    lf = sm.make_likelihood_function(tree, digits=2)
    lf.set_param_rule("omega", is_constant=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:160: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    sm = get_model("CNFGTR")
    lf = sm.make_likelihood_function(tree, digits=2)
    lf.set_param_rule("omega", init=0.1)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:175: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    sm = get_model("CNFGTR")
    lf = sm.make_likelihood_function(tree, digits=2)
    lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:190: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    sm = get_model("F81")
    lf = sm.make_likelihood_function(tree)
    lf.set_param_rule("length", upper=1.0)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:207: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.evolve.models import get_model

    sm = get_model("GTR", with_rate=True, distribution="gamma")
    tree = load_tree("data/primate_brca1.tree")
    lf = sm.make_likelihood_function(tree, bins=4, digits=2)
    lf.set_param_rule("bprobs", is_constant=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:222: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree
    from cogent3.evolve.models import get_model

    sm = get_model("GTR", with_rate=True, distribution="gamma")
    tree = load_tree("data/primate_brca1.tree")
    lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2)
    lf.set_param_rule("bprobs", is_constant=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:239: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree, load_aligned_seqs
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    aln = load_aligned_seqs("data/primate_brca1.fasta")
    sm = get_model("F81")
    lf = sm.make_likelihood_function(tree, digits=3, space=2)
    lf.set_alignment(aln)
    lf.optimise(show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:253: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.optimise(local=True, max_restarts=5, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:259: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.optimise(local=False, global_tolerance=1.0, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:265: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:276: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree, load_aligned_seqs
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    aln = load_aligned_seqs("data/primate_brca1.fasta")
    sm = get_model("F81")
    lf = sm.make_likelihood_function(tree, digits=3, space=2)
    lf.set_alignment(aln)
    try:
        lf.optimise(
            show_progress=False,
            limit_action="raise",
            max_evaluations=10,
            return_calculator=True,
        )
    except ArithmeticError as err:
        print(err)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:303: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree, load_aligned_seqs
    from cogent3.evolve.models import get_model

    sm = get_model("GTR")
    tree = load_tree("data/primate_brca1.tree")
    lf = sm.make_likelihood_function(tree)
    aln = load_aligned_seqs("data/primate_brca1.fasta")
    lf.set_alignment(aln)
    lf.optimise(local=True, show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:321: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lnL = lf.lnL
    lnL
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:326: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    nfp = lf.nfp
    nfp
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:338: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.get_aic()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:344: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.get_aic(second_order=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:353: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.get_bic()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:367: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    a_g = lf.get_param_value("A/G")
    a_g
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:372: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    human = lf.get_param_value("length", "Human")
    human
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:380: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    mprobs = lf.get_motif_probs()
    mprobs
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:388: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tables = lf.get_statistics(with_motif_probs=True, with_titles=True)
    tables[0]  # just displaying the first
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:398: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree, load_aligned_seqs
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    aln = load_aligned_seqs("data/primate_brca1.fasta")
    sm = get_model("F81")
    lf = sm.make_likelihood_function(tree, digits=3, space=2)
    lf.set_alignment(aln)
    lf.set_param_rule(
        "length",
        tip_names=["Human", "Chimpanzee"],
        outgroup_name="Galago",
        clade=True,
        is_independent=False,
    )
    lf.set_name("Null Hypothesis")
    lf.optimise(local=True, show_progress=False)
    null_lnL = lf.lnL
    null_nfp = lf.nfp
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:423: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule("length", is_independent=True)
    lf.set_name("Alt Hypothesis")
    lf.optimise(local=True, show_progress=False)
    alt_lnL = lf.lnL
    alt_nfp = lf.nfp
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:434: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.stats import chisqprob

    LR = 2 * (alt_lnL - null_lnL)  # the likelihood ratio statistic
    df = alt_nfp - null_nfp  # the test degrees of freedom
    p = chisqprob(LR, df)
    print(f"LR={LR:.4f} ; df={df}; p={df:.4f}")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:450: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree, load_aligned_seqs
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    aln = load_aligned_seqs("data/primate_brca1.fasta")

    sm = get_model("F81")
    lf = sm.make_likelihood_function(tree, digits=3, space=2)
    lf.set_alignment(aln)
    lf.set_param_rule(
        "length",
        tip_names=["Human", "Chimpanzee"],
        outgroup_name="Galago",
        clade=True,
        is_independent=False,
    )
    lf.set_name("Null Hypothesis")
    lf.optimise(local=True, show_progress=False)
    sim_aln = lf.simulate_alignment()
    sim_aln[:60]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:478: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree, load_aligned_seqs
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    aln = load_aligned_seqs("data/primate_brca1.fasta")
    sm = get_model("HKY85")
    lf = sm.make_likelihood_function(tree)
    lf.set_alignment(aln)
    lf.optimise(local=True, show_progress=False)
    kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa")
    print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}")
    human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human")
    print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:501: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree, load_aligned_seqs
    from cogent3.evolve.models import get_model

    aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG"))
    tree = make_tree(tip_names=aln.names)
    sm = get_model("F81")
    lf = sm.make_likelihood_function(tree)
    lf.set_alignment(aln)
    json = lf.to_json()
    json[:60]  # just truncating the displayed string
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:516: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.deserialise import deserialise_object

    newlf = deserialise_object(json)
    newlf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:528: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree, load_aligned_seqs
    from cogent3.evolve.models import get_model

    tree = load_tree("data/primate_brca1.tree")
    aln = load_aligned_seqs("data/primate_brca1.fasta")
    sm = get_model("F81")
    lf = sm.make_likelihood_function(tree, digits=3, space=2)
    lf.set_alignment(aln)
    lf.optimise(show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:542: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    ancestors = lf.likely_ancestral_seqs()
    ancestors[:60]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:549: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    ancestral_probs = lf.reconstruct_ancestral_seqs()
    ancestral_probs["root"][:5]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:4: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import get_code

    standard_code = get_code(1)
    standard_code.translate("TTTGCAAAC")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:16: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq, get_code

    standard_code = get_code(1)
    seq = make_seq("ATGCTAACATAAA", moltype="dna")
    translations = standard_code.sixframes(seq)
    print(translations)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq, get_code

    standard_code = get_code(1)
    seq = make_seq("ATGCTAACATAAA", moltype="dna")
    stops_frame1 = standard_code.get_stop_indices(seq, start=0)
    stops_frame1
    stop_index = stops_frame1[0]
    seq[stop_index : stop_index + 3]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:42: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq, get_code

    standard_code = get_code(1)
    standard_code["TTT"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:51: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    standard_code["A"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:58: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import get_code

    standard_code = get_code(1)
    standard_code["TTT"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:68: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import get_code

    standard_code = get_code(1)
    standard_code["A"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:78: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    targets = ["A", "C"]
    codons = [standard_code[aa] for aa in targets]
    codons
    flat_list = sum(codons, [])
    flat_list
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:89: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq

    my_seq = make_seq("AGTACACTGGTT", moltype="dna")
    sorted(my_seq.codon_alphabet())
    len(my_seq.codon_alphabet())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:102: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq

    my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna")
    codons = my_seq.get_in_motif_size(3)
    print(codons)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:115: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: AlphabetError

    pep = my_seq.get_translation()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:123: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq

    my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna")
    seq = my_seq.trim_stop_codon()
    pep = seq.get_translation()
    print(pep.to_fasta())
    print(type(pep))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:136: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_seq

    my_seq = make_seq("CAAATGTATTAA", name="my_gene", moltype="dna")
    pep = my_seq[:-3].get_translation()
    print(pep.to_fasta())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:16: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna")
    type(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:25: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln.info.source
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:38: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_unaligned_seqs

    seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna")
    type(seqs)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:50: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta")
    aln
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:62: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    protein_seqs = [">seq1", "DEKQL-RG", ">seq2", "DDK--SRG"]
    proteins_loaded = make_aligned_seqs(protein_seqs)
    proteins_loaded.moltype
    print(proteins_loaded)
    proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein")
    print(proteins_loaded)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:81: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"}
    seqs_loaded = make_aligned_seqs(seqs)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:91: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    seqs = [">seq1", "AATCG-A", ">seq2", "AATCGGA"]
    seqs_loaded = make_aligned_seqs(seqs)
    print(seqs_loaded)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:104: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    DNA_seqs = [
        ">sample1 Mus musculus",
        "AACCTGC--C",
        ">sample2 Gallus gallus",
        "AAC-TGCAAC",
    ]
    loaded_seqs = make_aligned_seqs(
        DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0]
    )
    loaded_seqs
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:124: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_unaligned_seqs

    seqs = {"seq1": "AATCA", "seq2": "AATCGGA"}
    seqs = make_unaligned_seqs(data=seqs, moltype="dna")
    seqs
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:144: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.fasta import MinimalFastaParser

    f = open("data/long_testseqs.fasta")
    seqs = [(name, seq) for name, seq in MinimalFastaParser(f)]
    seqs
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:157: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.fasta import LabelParser

    def latin_to_common(latin):
        return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin]

    label_parser = LabelParser(
        "%(species)s", [[1, "species", latin_to_common]], split_with=":"
    )
    for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc":
        label = label_parser(label)
        print(label, type(label))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:173: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.fasta import MinimalFastaParser, LabelParser

    fasta_data = [
        ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]",
        "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL",
        "SEIQNIKSELKYVPKAEQ",
        ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]",
        "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY",
        "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD",
    ]
    label_to_name = LabelParser(
        "%(ref)s",
        [[1, "gi", str], [3, "ref", str], [4, "description", str]],
        split_with="|",
    )
    for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name):
        print(name)
        print(name.info.gi)
        print(name.info.description)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv")
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:27: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv", sep="\t")
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:44: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import load_delimited

    header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t")
    rows[:4]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:54: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(with_header=False, sep="\t")
    rows = list(reader("data/CerebellumDukeDNaseSeq.pk"))
    rows[:4]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:70: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv", limit=2)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:82: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(
        lambda line: float(line[2]) <= 10, with_header=True, sep="\t"
    )
    table = load_table("data/stats.tsv", reader=reader, digits=1)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:94: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    reader = FilteringParser(
        lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True
    )
    table = load_table("data/stats.tsv", reader=reader, digits=1)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:107: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t")
    table = load_table("data/stats.tsv", reader=reader)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:117: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t")
    table = load_table("data/stats.tsv", reader=reader)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:132: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(with_header=True, sep="\t")
    data = list(reader("data/stats.tsv"))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:141: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    data[:2]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:150: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    header = ["A", "B", "C"]
    rows = [range(3), range(3, 6), range(6, 9), range(9, 12)]
    table = make_table(header=["A", "B", "C"], data=rows)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:164: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8])
    table = make_table(data=data)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:175: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = make_table(header=["C", "A", "B"], data=data)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:185: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv", index_name="Locus")
    table["NP_055852"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:190: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table["NP_055852", "Region"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:199: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from pandas import DataFrame

    from cogent3 import make_table

    data = dict(a=[0, 3], b=["a", "c"])
    df = DataFrame(data=data)
    table = make_table(data_frame=df)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:213: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]])
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:225: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    data = dict(a=[0, 3], b=["a", "c"])
    table = make_table(data=data)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:236: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    d2D = {
        "edge.parent": {
            "NineBande": "root",
            "edge.1": "root",
            "DogFaced": "root",
            "Human": "edge.0",
        },
        "x": {
            "NineBande": 1.0,
            "edge.1": 1.0,
            "DogFaced": 1.0,
            "Human": 1.0,
        },
        "length": {
            "NineBande": 4.0,
            "edge.1": 4.0,
            "DogFaced": 4.0,
            "Human": 4.0,
        },
    }
    table = make_table(
        data=d2D,
    )
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:268: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table(
        header=["abcd", "data"],
        data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]],
        missing_data="*",
        digits=1,
    )
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:283: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table()
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:17: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import available_moltypes

    available_moltypes()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:25: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import get_moltype

    dna = get_moltype("dna")
    dna
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:46: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dna.ambiguities
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dna.degenerates
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:60: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dna.complement("AGG")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:69: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seq = dna.make_seq("AGGCTT", name="seq1")
    seq
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:77: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rna = get_moltype("rna")
    rna.is_valid("ACGUACGUACGUACGU")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:87: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.core import moltype as mt

    DNAgapped = mt.MolType(
        seq_constructor=mt.DnaSequence,
        motifset=mt.IUPAC_DNA_chars,
        ambiguities=mt.IUPAC_DNA_ambiguities,
        complements=mt.IUPAC_DNA_ambiguities_complements,
        pairs=mt.DnaStandardPairs,
        gaps=".",
    )
    seq = DNAgapped.make_seq("ACG.")
    seq
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:104: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA
    from cogent3.core.sequence import DnaSequence

    DnaSequence.moltype = DNA
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/protein_sequences.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/protein_sequences.rst:14: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import PROTEIN

    p = PROTEIN.make_seq("THISISAPRQTEIN", "myProtein")
    type(p)
    str(p)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/protein_sequences.rst:25: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.core.genetic_code import DEFAULT as standard_code

    standard_code.translate("TTTGCAAAC")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/protein_sequences.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:14: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    print(tr.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:24: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    tr.write("data/temp.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    names = tr.get_node_names()
    names[:4]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:42: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    names[4:]
    names_nodes = tr.get_nodes_dict()
    names_nodes["Human"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tr.get_node_matching_name("Mouse")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:55: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    hu = tr.get_node_matching_name("Human")
    tr.name
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:63: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    hu.name
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:70: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    nodes = tr.get_nodes_dict()
    hu = nodes["Human"]
    type(hu)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:79: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    type(tr)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:88: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    nodes = tr.get_nodes_dict()
    for n in nodes.items():
        print(n)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:99: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    for n in tr.iter_tips():
        print(n)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:106: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    for n in tr.iter_nontips():
        print(n.get_newick())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:117: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    edges = tr.get_connecting_edges("edge.1", "Human")
    for edge in edges:
        print(edge.name)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:129: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    nodes = tr.get_nodes_dict()
    hu = nodes["Human"]
    mu = nodes["Mouse"]
    hu.distance(mu)
    hu.is_tip()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:143: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    nodes = tr.get_nodes_dict()
    hu = nodes["Human"]
    mu = nodes["Mouse"]
    lca = hu.last_common_ancestor(mu)
    lca
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:154: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    type(lca)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:161: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    hu = tr.get_node_matching_name("Human")
    for a in hu.ancestors():
        print(a.name)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:173: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    node = tr.get_node_matching_name("edge.1")
    children = list(node.iter_tips()) + list(node.iter_nontips())
    for child in children:
        print(child.name)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:186: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    dists = tr.get_distances()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:195: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    human_dists = [names for names in dists if "Human" in names]
    for dist in human_dists:
        print(dist, dists[dist])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:204: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    tr.max_tip_tip_distance()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:214: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    hu = tr.get_node_matching_name("Human")
    tips = hu.tips_within_distance(0.2)
    for t in tips:
        print(t)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:230: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    print(tr.rooted_at("edge.0").ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:240: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    print(tr.root_at_midpoint().ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:247: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(tr.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:254: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    print(tr.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:261: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(tr.rooted_with_tip("Mouse").ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:271: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    tr.get_newick()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:278: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tr.get_newick(with_distances=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:285: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    xml = tr.get_xml()
    for line in xml.splitlines():
        print(line)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:299: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    print(tr.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:309: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    for t in tr.preorder():
        print(t.get_newick())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:320: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    for t in tr.postorder():
        print(t.get_newick())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:334: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    for tip in tr.iter_nontips():
        tip_names = tip.get_tip_names()
        print(tip_names)
        sub_tree = tr.get_sub_tree(tip_names)
        print(sub_tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:348: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    from cogent3.util.misc import remove_files

    remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:364: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_tree

    simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;"
    simple_tree = make_tree(simple_tree_string)
    print(simple_tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:372: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    simple_tree.prune()
    print(simple_tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:377: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(simple_tree)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:384: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr1 = load_tree("data/test.tree")
    print(tr1.get_newick())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:391: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tr2 = tr1.unrooted_deepcopy()
    print(tr2.get_newick())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:401: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;"
    tr = make_tree(tree_string)
    print(tr.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:409: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(tr.bifurcating().ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:422: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = load_tree("data/test.tree")
    print(tr.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:429: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(tr.balanced().ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:438: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;")
    tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;")
    tr1.same_topology(tr2)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:452: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;")
    print(tr.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:459: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tr.set_tip_distances()
    for t in tr.preorder():
        print(t.name, t.TipDistance)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:468: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;")
    print(tr)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:475: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tr.scale_branch_lengths()
    print(tr)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:485: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr = make_tree("(B:3,(C:2,D:4)F:5)G;")
    d, tips = tr.tip_to_tip_distances()
    for i, t in enumerate(tips):
        print(t.name, d[i])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:505: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_tree

    tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;")
    tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;")
    tr1.compare_by_tip_distances(tr2)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
cookbook/loading_tabular.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
cookbook/loading_tabular.rst:11: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv")
    table
cookbook/loading_tabular.rst:27: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv", sep="\t")
    table
cookbook/loading_tabular.rst:44: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import load_delimited

    header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t")
    rows[:4]
cookbook/loading_tabular.rst:54: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(with_header=False, sep="\t")
    rows = list(reader("data/CerebellumDukeDNaseSeq.pk"))
    rows[:4]
cookbook/loading_tabular.rst:70: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv", limit=2)
    table
cookbook/loading_tabular.rst:82: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(
        lambda line: float(line[2]) <= 10, with_header=True, sep="\t"
    )
    table = load_table("data/stats.tsv", reader=reader, digits=1)
    table
cookbook/loading_tabular.rst:94: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    reader = FilteringParser(
        lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True
    )
    table = load_table("data/stats.tsv", reader=reader, digits=1)
    table
cookbook/loading_tabular.rst:107: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t")
    table = load_table("data/stats.tsv", reader=reader)
    table
cookbook/loading_tabular.rst:117: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t")
    table = load_table("data/stats.tsv", reader=reader)
    table
cookbook/loading_tabular.rst:132: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.parse.table import FilteringParser

    reader = FilteringParser(with_header=True, sep="\t")
    data = list(reader("data/stats.tsv"))
cookbook/loading_tabular.rst:141: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    data[:2]
cookbook/loading_tabular.rst:150: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    header = ["A", "B", "C"]
    rows = [range(3), range(3, 6), range(6, 9), range(9, 12)]
    table = make_table(header=["A", "B", "C"], data=rows)
    table
cookbook/loading_tabular.rst:164: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8])
    table = make_table(data=data)
    table
cookbook/loading_tabular.rst:175: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = make_table(header=["C", "A", "B"], data=data)
    table
cookbook/loading_tabular.rst:185: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv", index_name="Locus")
    table["NP_055852"]
cookbook/loading_tabular.rst:190: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table["NP_055852", "Region"]
cookbook/loading_tabular.rst:199: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from pandas import DataFrame

    from cogent3 import make_table

    data = dict(a=[0, 3], b=["a", "c"])
    df = DataFrame(data=data)
    table = make_table(data_frame=df)
    table
cookbook/loading_tabular.rst:213: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]])
    table
cookbook/loading_tabular.rst:225: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    data = dict(a=[0, 3], b=["a", "c"])
    table = make_table(data=data)
    table
cookbook/loading_tabular.rst:236: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    d2D = {
        "edge.parent": {
            "NineBande": "root",
            "edge.1": "root",
            "DogFaced": "root",
            "Human": "edge.0",
        },
        "x": {
            "NineBande": 1.0,
            "edge.1": 1.0,
            "DogFaced": 1.0,
            "Human": 1.0,
        },
        "length": {
            "NineBande": 4.0,
            "edge.1": 4.0,
            "DogFaced": 4.0,
            "Human": 4.0,
        },
    }
    table = make_table(
        data=d2D,
    )
    table
cookbook/loading_tabular.rst:268: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table(
        header=["abcd", "data"],
        data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]],
        missing_data="*",
        digits=1,
    )
    table
cookbook/loading_tabular.rst:283: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table()
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:21: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table()
    table.columns["a"] = [1, 3, 5]
    table.columns["b"] = [2, 4, 6]
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:35: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    data = dict(a=[0, 3], b=["a", "c"])
    table = make_table(data=data, title="Sample title", legend="a legend")
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:45: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    data = dict(a=[0, 3], b=["a", "c"])
    table = make_table(data=data)
    table.title = "My title"
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:57: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv")
    for row in table:
        print(row)
        break
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:68: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    for row in table:
        print(row["Locus"])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:78: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    data = dict(a=[0, 3, 5], b=["a", "c", "d"])
    table = make_table(data=data)
    table.shape[0] == 3
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:91: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.shape[1] == 2
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:100: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv")
    table.columns
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:107: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.columns["Region"]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:113: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    for name in table.columns:
        print(name)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:121: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:128: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table[:2, "Region":]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:135: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table[:2, :1]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:145: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv")
    table.format_column("Ratio", "%.1e")
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:158: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv", digits=1, space=2)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:165: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.space = "    "
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:175: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    h = ["name", "A/C", "A/G", "A/T", "C/A"]
    rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]]
    wrap_table = make_table(header=h, data=rows, max_width=30)
    wrap_table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:184: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name")
    wrap_table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:192: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = make_table(data=dict(a=list(range(10)), b=list(range(10))))
    table.head()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:199: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.head(2)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:208: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.tail()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:214: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.tail(1)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:221: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.set_repr_policy(random=3)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:229: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.set_repr_policy(head=2, tail=3)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:241: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    print(table.header)
    table = table.with_new_header("Ratio", "Stat")
    print(table.header)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:251: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table()
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:258: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.columns["a"] = [1, 3, 5]
    table.columns["b"] = [2, 4, 6]
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:269: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table = table.with_new_column(
        "LargeCon",
        lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0,
        columns=["Region", "Ratio"],
    )
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:282: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table.array
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:292: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    locus = table.tolist("Locus")
    locus
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:300: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.columns["Locus"].tolist()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:309: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    rows = table.tolist(["Region", "Locus"])
    rows
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:322: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table.to_dict()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:332: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table.columns.to_dict()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:340: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    df = table.to_dataframe()
    df
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:348: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    df = table.to_dataframe(categories="Region")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:357: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="")
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:362: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    contingency = table.to_categorical(["Ts", "Tv"])
    contingency
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:367: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    g_test = contingency.G_independence()
    g_test
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:374: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]})
    contingency = table.to_categorical(["Ts", "Tv"], index_name="")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:386: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table1 = load_table("data/stats.tsv")
    table2 = load_table("data/stats.tsv")
    table = table1.appended(None, table2)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:395: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table1.title = "Data1"
    table2.title = "Data2"
    table = table1.appended("Data#", table2, title="")
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:407: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table.summed("Ratio")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:414: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.columns["Ratio"].sum()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:423: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    all_numeric = make_table(
        header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)]
    )
    all_numeric
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:434: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    all_numeric.summed()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:440: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    all_numeric.summed(col_sum=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:449: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    mixed = make_table(
        header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]]
    )
    mixed
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:458: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    mixed.summed(strict=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:464: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    mixed.summed(col_sum=False, strict=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:473: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio")
    sub_table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:481: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    sub_table = table.filtered("Ratio < 10.0")
    sub_table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:488: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'")
    sub_table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:498: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20)
    big_numeric
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:506: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table.sorted(columns="Ratio")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:514: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.sorted(columns="Ratio", reverse="Ratio")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:521: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.sorted(columns=["Region", "Ratio"], reverse="Ratio")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:528: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    raw = table.tolist("Region")
    raw
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:537: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    raw = table.tolist(["Locus", "Region"])
    raw
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:546: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    assert table.distinct_values("Region") == set(["NonCon", "Con"])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:554: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    assert table.count("Region == 'NonCon' and Ratio > 1") == 1
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:564: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    table = make_table(
        data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"])
    )
    unique = table.count_unique("A")
    type(unique)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:574: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    unique
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:580: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    unique = table.count_unique(["A", "B"])
    unique
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:585: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    r = unique.to_table()
    r
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:595: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rows = [
        ["NP_004893", True],
        ["NP_005079", True],
        ["NP_005500", False],
        ["NP_055852", False],
    ]
    region_type = make_table(header=["Locus", "LargeCon"], data=rows)
    stats_table = load_table("data/stats.tsv")
    new = stats_table.joined(region_type, columns_self="Locus")
    new
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:615: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_table

    header = ["#OTU ID", "14SK041", "14SK802"]
    rows = [
        [-2920, "332", 294],
        [-1606, "302", 229],
        [-393, 141, 125],
        [-2109, 138, 120],
    ]
    table = make_table(header=header, rows=rows)
    table
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:631: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID")
    tp
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:641: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv", format="md")
    print(table)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:653: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv", format="tex")
    print(table)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:665: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    print(table.to_markdown(justify="ccr"))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:673: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table(
        "data/stats.tsv", title="Some stats.", legend="Derived from something."
    )
    print(table.to_latex(justify="ccr", label="tab:table1"))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:683: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table(
        "data/stats.tsv", title="Some stats.", legend="Derived from something."
    )
    print(table.to_rst(csv_table=True))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:693: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table(
        "data/stats.tsv", title="Some stats.", legend="Derived from something."
    )
    print(table.to_rst())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:705: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    print(table.to_string(format="latex"))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:715: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    rows = [
        ["1", 100, 101, 1.123],
        ["1", 101, 102, 1.123],
        ["1", 102, 103, 1.123],
        ["1", 103, 104, 1.123],
        ["1", 104, 105, 1.123],
        ["1", 105, 106, 1.123],
        ["1", 106, 107, 1.123],
        ["1", 107, 108, 1.123],
        ["1", 108, 109, 1],
        ["1", 109, 110, 1],
        ["1", 110, 111, 1],
        ["1", 111, 112, 1],
        ["1", 112, 113, 1],
        ["1", 113, 114, 1],
        ["1", 114, 115, 1],
        ["1", 115, 116, 1],
        ["1", 116, 117, 1],
        ["1", 117, 118, 1],
        ["1", 118, 119, 2],
        ["1", 119, 120, 2],
        ["1", 120, 121, 2],
        ["1", 150, 151, 2],
        ["1", 151, 152, 2],
        ["1", 152, 153, 2],
        ["1", 153, 154, 2],
        ["1", 154, 155, 2],
        ["1", 155, 156, 2],
        ["1", 156, 157, 2],
        ["1", 157, 158, 2],
        ["1", 158, 159, 2],
        ["1", 159, 160, 2],
        ["1", 160, 161, 2],
    ]
    bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:754: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    bgraph.head()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:760: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(
        bgraph.to_string(
            format="bedgraph",
            name="test track",
            description="test of bedgraph",
            color=(255, 0, 0),
            digits=0,
        )
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:775: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_table

    table = load_table("data/stats.tsv")
    straight_html = table.to_html()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:787: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.format.table import known_formats

    known_formats
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:796: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table.write("stats_tab.tex", justify="ccr", label="tab:table1")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:805: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    table = load_table("data/stats.tsv")
    table.write("stats_tab.txt", sep="\t")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:812: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import pathlib

    for name in ("stats_tab.txt", "stats_tab.tex"):
        p = pathlib.Path(name)
        if p.exists():
            p.unlink()
cookbook/union_dict.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.union_dict import UnionDict

    data = UnionDict(a=2, b={"c": 24, "d": [25]})
    data.a
cookbook/union_dict.rst:20: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    data["a"]
cookbook/union_dict.rst:24: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    data.b.d
cookbook/union_dict.rst:33: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.union_dict import UnionDict

    data = UnionDict(a=2, b={"c": 24, "d": [25]})
    data.b |= {"d": 25}
    data.b
cookbook/union_dict.rst:43: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    data.b.union({"d": [25]})
cookbook/union_dict.rst:47: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    data.b
    {"c": 24, "d": [25]}
cookbook/union_dict.rst:55: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: KeyError

    from cogent3.util.union_dict import UnionDict

    data = UnionDict(a=2, b={"c": 24, "d": [25]})
    data["k"]
cookbook/union_dict.rst:65: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: AttributeError

    data.k
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:16: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    import numpy

    def DiffOmega(omega):
        def omega_from_S(S):
            omega_est = S / (1 - numpy.e ** (-1 * S))
            return abs(omega - omega_est) ** 2

        return omega_from_S

    omega = 0.1
    f = DiffOmega(omega)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:32: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.optimisers import minimise, maximise

    S = minimise(
        f,  # the function
        xinit=1.0,  # the initial value
        bounds=(-100, 100),  # [lower,upper] bounds for the parameter
        local=True,  # just local optimisation, not Simulated Annealing
        show_progress=False,
    )
    assert 0.0 <= f(S) < 1e-6
    print("S=%.4f" % S)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:58: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: TypeError

    from cogent3.util.misc import iterable

    my_var = 10
    for i in my_var:
        print("will not work")

    for i in iterable(my_var):
        print(i)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:75: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import curry

    def foo(x, y):
        """Some function"""
        return x + y

    bar = curry(foo, 5)
    print(bar.__doc__)
    bar(10)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:92: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import is_iterable

    can_iter = [1, 2, 3, 4]
    cannot_iter = 1.234
    is_iterable(can_iter)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:100: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    is_iterable(cannot_iter)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:109: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import is_char

    class foo:
        pass

    is_char("a")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:118: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    is_char("ab")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:122: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    is_char(foo())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:131: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import recursive_flatten

    l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:137: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    recursive_flatten(l)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:146: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import not_list_tuple

    not_list_tuple(1)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:152: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    not_list_tuple([1])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:156: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    not_list_tuple("ab")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:165: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import add_lowercase

    d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"}
    add_lowercase(d)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:177: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import DistanceFromMatrix
    from numpy import array

    m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
    f = DistanceFromMatrix(m)
    f(0, 0)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:186: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    f(1, 2)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:195: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import ClassChecker

    class not_okay(object):
        pass

    no = not_okay()

    class okay(object):
        pass

    o = okay()

    class my_dict(dict):
        pass

    md = my_dict()
    cc = ClassChecker(str, okay, dict)
    o in cc
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:216: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    no in cc
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:220: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    5 in cc
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:224: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    {"a": 5} in cc
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:228: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    "asasas" in cc
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:232: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    md in cc
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:241: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import Delegator

    class ListAndString(list, Delegator):
        def __init__(self, items, string):
            Delegator.__init__(self, string)
            for i in items:
                self.append(i)

    ls = ListAndString([1, 2, 3], "ab_cd")
    len(ls)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:254: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    ls[0]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:258: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    ls.upper()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:262: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    ls.split("_")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:271: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import FunctionWrapper

    f = FunctionWrapper(str)
    f
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:278: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    f(123)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:289: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.util.misc import ConstrainedDict

    d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc")
    d
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:296: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: ConstraintError

    d["d"] = 5
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:10: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import available_codes

    available_codes()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:20: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs

    nt_seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna")
    nt_seqs[:21]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:29: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aa_seqs = nt_seqs.get_translation(gc=1, incomplete_ok=True)
    aa_seqs[:20]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/cookbook/what_codes.rst:39: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import get_code

    gc = get_code(4)
    gc
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/align_codons_to_protein.rst:8: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_unaligned_seqs, make_aligned_seqs
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/align_codons_to_protein.rst:14: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    seqs = {
        "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT",
        "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG",
        "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA",
    }
    unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna")
    print(unaligned_DNA.to_fasta())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/align_codons_to_protein.rst:26: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    unaligned_aa = unaligned_DNA.get_translation()
    print(unaligned_aa.to_fasta())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/align_codons_to_protein.rst:33: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aligned_aa_seqs = {
        "hum": "KQIQESSENGSLAARQERQAQVNLT",
        "mus": "KQIQESGESGSLAARQERQAQVNLT",
        "rat": "LNKQ------PLS---------NKK",
    }
    aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein")
    aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA)
    aligned_DNA
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:15: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs
    from cogent3.evolve import distance
    from cogent3.cluster.UPGMA import upgma
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:23: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import HKY85
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:29: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    al = load_aligned_seqs("data/test.paml")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:35: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    d = distance.EstimateDistances(al, submodel=HKY85())
    d.run(show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:42: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    mycluster = upgma(d.get_pairwise_distances())
    print(mycluster.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:49: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    mycluster.write("test_upgma.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:55: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import os

    os.remove("test_upgma.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs
    from cogent3.evolve import distance
    from cogent3.phylo import nj
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:21: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import get_model
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:27: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    al = load_aligned_seqs("data/long_testseqs.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:33: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    d = distance.EstimateDistances(al, submodel=get_model("HKY85"))
    d.run(show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:40: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    mytree = nj.nj(d.get_pairwise_distances(), show_progress=False)
    print(mytree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:47: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    mytree.write("test_nj.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import os

    os.remove("test_nj.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:15: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs
    from cogent3.evolve import distance
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:22: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import HKY85
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    al = load_aligned_seqs("data/long_testseqs.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    d = distance.EstimateDistances(al, submodel=HKY85())
    d.run(show_progress=False)
    d.get_pairwise_distances()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:44: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    d.write("dists_for_phylo.phylip", format="phylip")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:52: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    import pickle

    with open("dists_for_phylo.pickle", "wb") as f:
        pickle.dump(d.get_pairwise_distances(), f)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/calculate_pairwise_distances.rst:61: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import os

    for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle":
        os.remove(file_name)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import get_model
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:42: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tf = get_model("GY94")
    nf = get_model("MG94GTR")
    cnf = get_model("CNFGTR")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:52: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, load_tree

    aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna")
    tree = load_tree("data/primate_brca1.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:64: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf = cnf.make_likelihood_function(tree, digits=2, space=3)
    lf.set_param_rule("omega", is_constant=True, value=1.0)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:73: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    optimiser_args = dict(
        local=True, max_restarts=5, tolerance=1e-8, show_progress=False
    )
    lf.set_alignment(aln)
    lf.optimise(**optimiser_args)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:92: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    neutral_lnL = lf.get_log_likelihood()
    neutral_nfp = lf.get_num_free_params()
    lf.set_param_rule("omega", is_constant=False)
    lf.optimise(**optimiser_args)
    non_neutral_lnL = lf.get_log_likelihood()
    non_neutral_nfp = lf.get_num_free_params()
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:104: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.stats import chisqprob

    LR = 2 * (non_neutral_lnL - neutral_lnL)
    df = non_neutral_nfp - neutral_nfp
    print(chisqprob(LR, df))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:114: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule(
        "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True
    )
    lf.optimise(**optimiser_args)
    lf
    chimp_human_clade_lnL = lf.get_log_likelihood()
    chimp_human_clade_nfp = lf.get_num_free_params()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:124: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL)
    df = chimp_human_clade_nfp - non_neutral_nfp
    print(chisqprob(LR, df))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:137: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf = cnf.make_likelihood_function(tree, digits=2, space=3)
    lf.set_alignment(aln)
    lf.optimise(**optimiser_args)
    non_neutral_lnL = lf.get_log_likelihood()
    non_neutral_nfp = lf.get_num_free_params()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:149: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    annot_tree = lf.get_annotated_tree()
    omega_mle = lf.get_param_value("omega")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:156: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_lf = cnf.make_likelihood_function(
        annot_tree, bins=["neutral", "adaptive"], digits=2, space=3
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:164: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    epsilon = 1e-6
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:170: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle)
    rate_lf.set_param_rule(
        "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:179: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:185: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_lf.set_alignment(aln)
    rate_lf.optimise(**optimiser_args)
    rate_lnL = rate_lf.get_log_likelihood()
    rate_nfp = rate_lf.get_num_free_params()
    LR = 2 * (rate_lnL - non_neutral_lnL)
    df = rate_nfp - non_neutral_nfp
    rate_lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:195: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(chisqprob(LR, df))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:201: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    pp = rate_lf.get_bin_probs()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:212: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    from numpy import array
    from cogent3 import make_table
    from IPython.core.display import HTML

    header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges']
    data = {'Site Class': array(['0', '1', '2a', '2b'], dtype='<U2'), 'Proportion': array(['p0', 'p1', 'p2', 'p3'], dtype='<U2'), 'Background Edges': array(['0 < omega0 < 1', 'omega1 = 1', '0 < omega0 < 1', 'omega1 = 1'],
      dtype='<U14'), 'Foreground Edges': array(['0 < omega0 < 1', 'omega1 = 1', '0 < omega2 > 1', '0 < omega0 < 1'],
      dtype='<U14')}
    data = {k: array(data[k], dtype='U') for k in data}
    table = make_table(header, data=data)
    HTML(table.set_repr_policy(show_shape=False))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:231: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_lf = cnf.make_likelihood_function(tree, bins=["0", "1"], digits=2, space=3)
    rate_lf.set_param_rule("omega", bin="0", upper=1.0 - epsilon, init=1 - epsilon)
    rate_lf.set_param_rule("omega", bins="1", is_constant=True, value=1.0)
    rate_lf.set_alignment(aln)
    rate_lf.optimise(**optimiser_args)
    tables = rate_lf.get_statistics(with_titles=True)
    for table in tables:
        if "bin" in table.title:
            print(table)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:245: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    globals = [t for t in tables if "global" in t.title][0]
    globals = dict(zip(globals.header, globals.tolist()[0]))
    bin_params = [t for t in tables if "bin" in t.title][0]
    rate_class_omegas = dict(bin_params.tolist(["bin", "omega"]))
    rate_class_probs = dict(bin_params.tolist(["bin", "bprobs"]))
    lengths = [t for t in tables if "edge" in t.title][0]
    lengths = dict(lengths.tolist(["edge", "length"]))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:257: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_branch_lf = cnf.make_likelihood_function(
        tree, bins=["0", "1", "2a", "2b"], digits=2, space=3
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:265: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    for branch, length in lengths.items():
        rate_branch_lf.set_param_rule("length", edge=branch, init=length)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:272: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    for param, mle in globals.items():
        rate_branch_lf.set_param_rule(param, init=mle)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:279: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_branch_lf.set_param_rule(
        "omega", bins=["0", "2a"], upper=1.0, init=rate_class_omegas["0"]
    )
    rate_branch_lf.set_param_rule(
        "omega", bins=["1", "2b"], is_constant=True, value=1.0
    )
    rate_branch_lf.set_param_rule(
        "omega",
        bins=["2a", "2b"],
        edges=["Chimpanzee", "Human"],
        init=99,
        lower=1.0,
        upper=100.0,
        is_constant=False,
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:299: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_branch_lf.set_param_rule(
        "bprobs",
        init=[
            rate_class_probs["0"] - epsilon,
            rate_class_probs["1"] - epsilon,
            epsilon,
            epsilon,
        ],
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:313: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    rate_branch_lf.set_alignment(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:10: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs
    from cogent3.core.alignment import ArrayAlignment
    from cogent3.evolve.coevolution import validate_alignment

    aln = make_aligned_seqs(
        {"1": "GAA", "2": "CTA", "3": "CTC", "4": "-TC"},
        moltype="protein",
        array_align=True,
    )
    validate_alignment(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:25: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs
    from cogent3.core.alignment import ArrayAlignment

    aln = make_aligned_seqs(
        {"1": "AAA", "2": "CTA", "3": "CTC", "4": "-TC"},
        moltype="protein",
        array_align=True,
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:38: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.coevolution import coevolve_pair_functions, coevolve_pair

    coevolve_pair(coevolve_pair_functions["mi"], aln, pos1=1, pos2=2)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:46: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.coevolution import coevolve_pair_functions, coevolve_pair

    coevolve_pair(coevolve_pair_functions["sca"], aln, pos1=1, pos2=2, cutoff=0.5)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:54: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.coevolution import (
        coevolve_position_functions,
        coevolve_position,
    )

    coevolve_position(coevolve_position_functions["mi"], aln, position=1)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:65: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.coevolution import (
        coevolve_alignment_functions,
        coevolve_alignment,
    )

    coevolve_alignment(coevolve_alignment_functions["mi"], aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:76: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(coevolve_pair_functions.keys())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:82: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.coevolution import (
        coevolve_alignment_functions,
        coevolve_alignments,
    )

    aln1 = make_aligned_seqs(
        {
            "human+protein1": "AAA",
            "pig+protein1": "CTA",
            "chicken+protein1": "CTC",
            "echidna+weird_db_identifier": "-TC",
        },
        moltype="protein",
        array_align=True,
    )
    aln2 = make_aligned_seqs(
        {
            "pig+protein2": "AAAY",
            "chicken+protein2": "CTAY",
            "echidna+protein2": "CTCF",
            "human+protein2": "-TCF",
        },
        moltype="protein",
        array_align=True,
    )
    coevolve_alignments(coevolve_alignment_functions["mi"], aln1, aln2)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:8: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA
    from cogent3.core.annotation import Feature

    s = DNA.make_seq("AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAAAAAAAAA", name="Orig")
    exon1 = s.add_annotation(Feature, "exon", "fred", [(10, 15)])
    exon2 = s.add_annotation(Feature, "exon", "trev", [(30, 40)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:19: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    s[exon1]
    exon1.get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:26: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    exons = s.get_annotations_matching("exon")
    print(exons)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:33: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    dont_exist = s.get_annotations_matching("dont_exist")
    dont_exist
    s[dont_exist]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:41: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(s.get_region_covering_all(exons))
    print(s.get_region_covering_all(exons).get_shadow())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    s.get_region_covering_all(exons).get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:54: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    s[exon1, exon2]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:60: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: ValueError

    print(s.get_region_covering_all(exons + exons))
    s[exon1, exon1, exon1, exon1, exon1]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:68: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: ValueError

    s[15:20, 5:16]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:75: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    exon1[0:3].get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:81: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    c = s[exon1[4:]] + s
    print(len(c))
    for feat in c.annotations:
        print(feat)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:90: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :raises: ValueError

    print(c[exon1])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:97: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    len(s.annotations)
    region = s.get_region_covering_all(exons)
    len(s.annotations)
    region.attach()
    len(s.annotations)
    region.detach()
    len(s.annotations)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:109: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    plus = DNA.make_seq("AAGGGGAAAACCCCCAAAAAAAAAATTTTTTTTTTAAA", name="plus")
    plus_cds = plus.add_annotation(Feature, "CDS", "gene", [(2, 6), (10, 15), (25, 35)])
    print(plus_cds.get_slice())
    minus = plus.rc()
    minus_cds = minus.get_annotations_matching("CDS")[0]
    print(minus_cds.get_slice())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:120: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_aligned_seqs

    aln = make_aligned_seqs(
        [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
    )
    print(aln)
    exon = aln.get_seq("x").add_annotation(Feature, "exon", "fred", [(3, 8)])
    aln_exons = aln.get_annotations_from_seq("x", "exon")
    aln_exons = aln.get_annotations_from_any_seq("exon")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:134: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(exon)
    print(aln_exons[0])
    print(aln_exons[0].get_slice())
    aln_exons[0].attach()
    len(aln.annotations)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:144: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    exons = aln.get_projected_annotations("y", "exon")
    print(exons)
    print(aln.get_seq("y")[exons[0].map.without_gaps()])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:152: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        [["x", "-AAAAAAAAA"], ["y", "TTTT--CCCC"]], array_align=False
    )
    s = DNA.make_seq("AAAAAAAAA", name="x")
    exon = s.add_annotation(Feature, "exon", "fred", [(3, 8)])
    exon = aln.get_seq("x").copy_annotations(s)
    aln_exons = list(aln.get_annotations_from_seq("x", "exon"))
    print(aln_exons)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:165: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    exon = aln.get_seq("y").copy_annotations(s)
    aln_exons = list(aln.get_annotations_from_seq("y", "exon"))
    print(aln_exons)
    print(aln[aln_exons])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:174: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs([["x", "-AAAA"], ["y", "TTTTT"]], array_align=False)
    seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
    exon = seq.add_feature("exon", "A", [(5, 8)])
    aln.get_seq("x").copy_annotations(seq)
    copied = list(aln.get_annotations_from_seq("x", "exon"))
    copied
    copied[0].get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:186: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
    )
    seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCC", "x")
    match_exon = seq.add_feature("exon", "A", [(5, 8)])
    aln.get_seq("y").copy_annotations(seq)
    copied = list(aln.get_annotations_from_seq("y", "exon"))
    copied
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:199: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        [["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False
    )
    diff_len_seq = DNA.make_seq("CCCCCCCCCCCCCCCCCCCCCCCCCCCC", "x")
    nonmatch = diff_len_seq.add_feature("repeat", "A", [(12, 14)])
    aln.get_seq("y").copy_annotations(diff_len_seq)
    copied = list(aln.get_annotations_from_seq("y", "repeat"))
    copied
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:212: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        [["x", "-AAAAAAAAA"], ["y", "------TTTT"]], array_align=False
    )
    exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)])
    aln_exons = list(aln.get_annotations_from_seq("x", "exon"))
    print(aln_exons)
    print(aln_exons[0].get_slice())
    aln = make_aligned_seqs(
        [["x", "-AAAAAAAAA"], ["y", "TTTT--T---"]], array_align=False
    )
    exon = aln.get_seq("x").add_feature("exon", "fred", [(3, 8)])
    aln_exons = list(aln.get_annotations_from_seq("x", "exon"))
    print(aln_exons[0].get_slice())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:230: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        [["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], moltype="dna", array_align=False
    )
    print(aln)
    exon = aln.get_seq("x").add_feature("exon", "ex1", [(0, 4)])
    print(exon)
    print(exon.get_slice())
    aln_exons = list(aln.get_annotations_from_seq("x", "exon"))
    print(aln_exons)
    print(aln_exons[0].get_slice())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:245: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(aln_exons[0].as_one_span().get_slice())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:251: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln_rc = aln.rc()
    rc_exons = list(aln_rc.get_annotations_from_any_seq("exon"))
    print(aln_rc[rc_exons])  # not using as_one_span, so gap removed from x
    print(aln_rc[rc_exons[0].as_one_span()])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:260: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    all_exons = aln.get_region_covering_all(aln_exons)
    coords = all_exons.get_coordinates()
    assert coords == [(0, 1), (2, 5)]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:270: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = make_aligned_seqs(
        [["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], array_align=False
    )
    print(aln)
    exon = aln.get_seq("x").add_feature("exon", "norwegian", [(0, 4)])
    print(exon.get_slice())
    repeat = aln.get_seq("x").add_feature("repeat", "blue", [(9, 12)])
    print(repeat.get_slice())
    repeat = aln.get_seq("y").add_feature("repeat", "frog", [(5, 7)])
    print(repeat.get_slice())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:285: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?"))
    print(aln.get_seq("x").with_masked_annotations("exon", mask_char="?", shadow=True))
    print(aln.get_seq("x").with_masked_annotations(["exon", "repeat"], mask_char="?"))
    print(
        aln.get_seq("x").with_masked_annotations(
            ["exon", "repeat"], mask_char="?", shadow=True
        )
    )
    print(aln.get_seq("y").with_masked_annotations("exon", mask_char="?"))
    print(aln.get_seq("y").with_masked_annotations("repeat", mask_char="?"))
    print(
        aln.get_seq("y").with_masked_annotations("repeat", mask_char="?", shadow=True)
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:303: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(aln.with_masked_annotations("exon", mask_char="?"))
    print(aln.with_masked_annotations("exon", mask_char="?", shadow=True))
    print(aln.with_masked_annotations("repeat", mask_char="?"))
    print(aln.with_masked_annotations("repeat", mask_char="?", shadow=True))
    print(aln.with_masked_annotations(["repeat", "exon"], mask_char="?"))
    print(aln.with_masked_annotations(["repeat", "exon"], shadow=True))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:314: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    data = [["human", "CGAAACGTTT"], ["mouse", "CTAAACGTCG"]]
    as_series = make_aligned_seqs(data, array_align=False)
    as_items = make_aligned_seqs(data, array_align=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:322: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    as_series.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2), (5, 7)])
    as_series.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7), (8, 10)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:329: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    as_items.get_seq("human").add_feature("cpgsite", "cpg", [(0, 2)])
    as_items.get_seq("human").add_feature("cpgsite", "cpg", [(5, 7)])
    as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(5, 7)])
    as_items.get_seq("mouse").add_feature("cpgsite", "cpg", [(8, 10)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:338: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    serial = as_series.with_masked_annotations(["cpgsite"])
    print(serial)
    itemwise = as_items.with_masked_annotations(["cpgsite"])
    print(itemwise)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:347: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(plus.with_masked_annotations("CDS"))
    print(minus.with_masked_annotations("CDS"))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/empirical_protein_models.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/empirical_protein_models.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, make_tree
    from cogent3.evolve.substitution_model import EmpiricalProteinMatrix
    from cogent3.parse.paml_matrix import PamlMatrixParser
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/empirical_protein_models.rst:21: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    treestring = "(((rabbit,rat),human),goat-cow,marsupial);"
    t = make_tree(treestring)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/empirical_protein_models.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    al = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/empirical_protein_models.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    matrix_file = open("data/dayhoff.dat")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/empirical_protein_models.rst:40: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    empirical_matrix, empirical_frequencies = PamlMatrixParser(matrix_file)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/empirical_protein_models.rst:46: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    sm = EmpiricalProteinMatrix(empirical_matrix, empirical_frequencies)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/empirical_protein_models.rst:52: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf = sm.make_likelihood_function(t)
    lf.set_alignment(al)
    lf.optimise(show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:21: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.substitution_model import TimeReversibleNucleotide, predicate
    from cogent3 import load_aligned_seqs, load_tree
    from cogent3.maths.stats import chisqprob
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:29: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    tree = load_tree("data/test.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:39: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    MotifChange = predicate.MotifChange
    treat_gap = dict(recode_gaps=True, model_gaps=False)
    kappa = (~MotifChange("R", "Y")).aliased("kappa")
    model = TimeReversibleNucleotide(predicates=[kappa], **treat_gap)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf_one = model.make_likelihood_function(tree, digits=2, space=3)
    lf_one.set_alignment(aln)
    lf_one.optimise(show_progress=False)
    lnL_one = lf_one.get_log_likelihood()
    df_one = lf_one.get_num_free_params()
    lf_one
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:62: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    bin_submod = TimeReversibleNucleotide(
        predicates=[kappa], ordered_param="rate", distribution="gamma", **treat_gap
    )
    lf_bins = bin_submod.make_likelihood_function(
        tree, bins=2, sites_independent=True, digits=2, space=3
    )
    lf_bins.set_param_rule("bprobs", is_constant=True)
    lf_bins.set_alignment(aln)
    lf_bins.optimise(local=True, show_progress=False)
    lnL_bins = lf_bins.get_log_likelihood()
    df_bins = lf_bins.get_num_free_params()
    assert df_bins == 9
    lf_bins
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:83: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf_patches = bin_submod.make_likelihood_function(
        tree, bins=2, sites_independent=False, digits=2, space=3
    )
    lf_patches.set_param_rule("bprobs", is_constant=True)
    lf_patches.set_alignment(aln)
    lf_patches.optimise(local=True, show_progress=False)
    lnL_patches = lf_patches.get_log_likelihood()
    df_patches = lf_patches.get_num_free_params()
    lf_patches
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:97: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    LR = lambda alt, null: 2 * (alt - null)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:103: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lr = LR(lnL_bins, lnL_one)
    lr
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:108: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print("%.4f" % chisqprob(lr, df_patches - df_bins))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:114: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    bprobs = lf_patches.get_param_value("bprobs")
    print("%.1f : %.1f" % tuple(bprobs))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:121: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    pp = lf_patches.get_bin_probs()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:127: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(pp["bin0"][20])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:140: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from numpy import array

    single_kappa = lf_one.get_param_value("kappa")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:148: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    kappa_bin_submod = TimeReversibleNucleotide(predicates=[kappa], **treat_gap)
    lf_kappa = kappa_bin_submod.make_likelihood_function(
        tree, bins=["slow", "fast"], sites_independent=False, digits=1, space=3
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:157: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    epsilon = 1e-6
    lf_kappa.set_param_rule(
        kappa, init=single_kappa - epsilon, upper=single_kappa, bin="slow"
    )
    lf_kappa.set_param_rule(
        kappa, init=single_kappa + epsilon, lower=single_kappa, bin="fast"
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/hmm_par_heterogeneity.rst:169: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf_kappa.set_param_rule("bprobs", init=array([1.0 - epsilon, 0.0 + epsilon]))
    lf_kappa.set_alignment(aln)
    lf_kappa.optimise(local=True, show_progress=False)
    lf_kappa
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:8: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.core.tree import PhyloNode
    from cogent3 import load_tree, make_tree
    from cogent3.parse.tree import DndParser
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:24: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    simple_tree_string = "(B:0.2,(C:0.3,D:0.4)E:0.5)F;"
    complex_tree_string = "(((363564 AB294167.1 Alkalibacterium putridalgicola:0.0028006,55874 AB083411.1 Marinilactibacillus psychrotolerans:0.0022089):0.40998,(15050 Y10772.1 Facklamia hominis:0.32304,(132509 AY707780.1 Aerococcus viridans:0.58815,((143063 AY879307.1 Abiotrophia defectiva:0.5807,83619 AB042060.1 Bacillus schlegelii:0.23569):0.03586,169722 AB275483.1 Fibrobacter succinogenes:0.38272):0.06516):0.03492):0.14265):0.63594,(3589 M62687.1 Fibrobacter intestinalis:0.65866,314063 CP001146.1 Dictyoglomus thermophilum:0.38791):0.32147,276579 EU652053.1 Thermus scotoductus:0.57336);"
    simple_tree = make_tree(simple_tree_string)
    complex_tree = DndParser(complex_tree_string, PhyloNode)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:35: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(simple_tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:41: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    A_node = PhyloNode(name="A", Length=0.1)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:47: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(simple_tree.children)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    simple_tree.children[1].remove("C")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:59: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    simple_tree.children[1].insert(0, A_node)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:65: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(simple_tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:71: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    simple_tree.children[1].remove("A")
    print(simple_tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:78: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    simple_tree.prune()
    print(simple_tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:90: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    for n in complex_tree.iter_tips():
        n.name = n.name.split()[2] + " " + n.name.split()[3]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:97: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(complex_tree.ascii_art(show_internal=False))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:105: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tips = complex_tree.tips()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:111: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    tips_to_delete = []
    AEROCOCCUS_INDEX = 3
    for n in tips:
        if tips[AEROCOCCUS_INDEX].distance(n) > 1.8:
            tips_to_delete.append(n)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:121: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    for n in tips_to_delete:
        n.parent.remove(n)
        complex_tree.prune()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/manipulating_tree_nodes.rst:129: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(complex_tree.ascii_art(show_internal=False))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, load_tree
    from cogent3.evolve.models import get_model
    from cogent3.maths import stats
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:21: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    al = load_aligned_seqs("data/long_testseqs.fasta")
    t = load_tree("data/test.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    sm = get_model("MG94GTR")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf = sm.make_likelihood_function(t, digits=2, space=2)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:40: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_alignment(al)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:46: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.optimise(global_tolerance=1.0, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:52: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:58: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    null_lnL = lf.get_log_likelihood()
    null_nfp = lf.get_num_free_params()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:65: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule("omega", is_independent=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:71: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.optimise(local=True, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:77: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:83: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    at = lf.get_annotated_tree()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:89: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    LR = 2 * (lf.get_log_likelihood() - null_lnL)
    df = lf.get_num_free_params() - null_nfp
    P = stats.chisqprob(LR, df)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:97: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(f"Likelihood ratio statistic = {LR}")
    print(f"degrees-of-freedom = {df}")
    print(f"probability = {P}")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:17: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, load_tree
    from cogent3.evolve import bootstrap
    from cogent3.evolve.models import HKY85
    from cogent3.maths import stats
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    def create_alt_function():
        t = load_tree("data/test.tree")
        sm = HKY85()
        return sm.make_likelihood_function(t)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:37: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    def create_null_function():
        lf = create_alt_function()
        # set the local clock for humans & howler monkey
        lf.set_local_clock("Human", "HowlerMon")
        return lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:47: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = load_aligned_seqs("data/long_testseqs.fasta")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    estimateP = bootstrap.EstimateProbability(
        create_null_function(), create_alt_function(), aln
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:61: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    estimateP.set_num_replicates(5)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:67: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    estimateP.run(show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:73: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    p = estimateP.get_estimated_prob()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/parametric_bootstrap.rst:79: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print("%.2f, %.2f" % estimateP.get_observed_lnL())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:26: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import numpy

    numpy.random.seed(11)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:33: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    import numpy

    t = numpy.arange(0, 10, 0.1)
    n = numpy.random.randn(len(t))
    nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1
    nse = nse[: len(t)]
    sig = numpy.sin(2 * numpy.pi * t) + nse
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.period import dft

    pwr, period = dft(sig)
    print(period)
    print(pwr)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:58: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    pwr = abs(pwr)
    max_pwr, max_period = sorted(zip(pwr, period))[-1]
    print(max_pwr, max_period)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:69: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.period import auto_corr

    pwr, period = auto_corr(sig)
    print(period)
    print(pwr)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:79: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    max_pwr, max_period = sorted(zip(pwr, period))[-1]
    print(max_pwr, max_period)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:89: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    s = (
        "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG"
        "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT"
        "AATTTTTAACCGCGGAATTGCGTC"
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:99: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.stats.period import SeqToSymbols

    seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"])
    symbols = seq_to_symbols(s)
    len(symbols) == len(s)
    symbols
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:110: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.period import ipdft

    powers, periods = ipdft(symbols)
    powers
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:117: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    periods
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:123: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.period import auto_corr, hybrid

    powers, periods = auto_corr(symbols)
    powers
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:130: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    periods
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:134: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    powers, periods = hybrid(symbols)
    powers
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:139: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    periods
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:151: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.period import goertzel

    pwr = goertzel(sig, 10)
    print(pwr)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:165: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    powers, periods = auto_corr(symbols)
    llim = 2
    period5 = 5 - llim
    periods[period5]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:172: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    powers[period5]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:178: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.period import goertzel

    period = 4
    power = goertzel(symbols, period)
    ipdft_powers, periods = ipdft(symbols)
    ipdft_power = abs(ipdft_powers[period - llim])
    round(power, 6) == round(ipdft_power, 6)
    power
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:191: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    power = hybrid(symbols, period=period)
    power
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:204: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.period import Goertzel

    goertzel_calc = Goertzel(len(sig), period=10)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:212: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.stats.period import blockwise_bootstrap

    obs_stat, p = blockwise_bootstrap(
        sig, calc=goertzel_calc, block_size=10, num_reps=1000
    )
    print(obs_stat)
    print(p)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:230: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.period import Hybrid

    hybrid_calculator = Hybrid(len(s), period=4)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:240: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.stats.period import SeqToSymbols

    seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:248: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.maths.stats.period import blockwise_bootstrap

    stat, p = blockwise_bootstrap(
        s,
        calc=hybrid_calculator,
        block_size=10,
        num_reps=1000,
        seq_to_symbols=seq_to_symbols,
    )
    print(stat)
    p < 0.1
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:15: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import pickle
    from cogent3 import load_aligned_seqs
    from cogent3.evolve import distance
    from cogent3.evolve.models import HKY85
    from cogent3.evolve.fast_distance import DistanceMatrix

    al = load_aligned_seqs("data/long_testseqs.fasta")
    d = distance.EstimateDistances(al, submodel=HKY85())
    d.run(show_progress=False)

    with open("dists_for_phylo.pickle", "wb") as f:
        pickle.dump(d.get_pairwise_distances(), f)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:31: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    import pickle
    from cogent3.phylo import least_squares
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:38: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    with open("dists_for_phylo.pickle", "rb") as f:
        dists = pickle.load(f)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:47: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    ls = least_squares.WLS(dists)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists))
    ls_pairwise_matrix = least_squares.WLS(dists.to_dict())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:65: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    score, tree = ls.trex(a=5, k=1, show_progress=False)
    assert score < 1e-4
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:77: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    trees = ls.trex(a=5, k=5, return_all=True, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:83: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(len(trees))
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:89: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    wls_stats = [tree[0] for tree in trees]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:101: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    t1 = trees[0][1].balanced()
    t2 = trees[1][1].balanced()
    print(t1.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:107: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(t2.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:118: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import make_tree

    query_tree = make_tree(
        "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)"
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:128: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    ls.evaluate_tree(query_tree)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:134: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    wls, t = ls.evaluate_topology(query_tree)
    assert "%.4f" % wls == "0.0084"
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:146: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import os

    os.remove("dists_for_phylo.pickle")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:15: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.substitution_model import TimeReversibleNucleotide
    from cogent3 import load_tree
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:22: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    model = TimeReversibleNucleotide(equal_motif_probs=True)
    tree = load_tree("data/test.tree")
    lf = model.make_likelihood_function(tree)
    lf.set_param_rule("length", value=0.6, is_constant=True)
    aln1 = lf.simulate_alignment(sequence_length=10000)
    lf.set_param_rule("length", value=0.2, is_constant=True)
    aln2 = lf.simulate_alignment(sequence_length=10000)
    aln3 = aln1 + aln2
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:35: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    model = TimeReversibleNucleotide(
        equal_motif_probs=True, ordered_param="rate", distribution="free"
    )
    lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3)
    lf.set_alignment(aln3)
    lf.optimise(local=True, max_restarts=2, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:46: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0]
    bprobs
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/rate_heterogeneity.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    model = TimeReversibleNucleotide(
        equal_motif_probs=True, ordered_param="rate", distribution="gamma"
    )
    lf = model.make_likelihood_function(tree, bins=4)
    lf.set_param_rule("bprobs", is_constant=True)
    lf.set_alignment(aln3)
    lf.optimise(local=True, max_restarts=2, show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, load_tree
    from cogent3.evolve.models import get_model
    from cogent3.maths import stats
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:21: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    t = load_tree(filename="data/test.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:28: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    sm = get_model("HKY85")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:34: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf = sm.make_likelihood_function(t, digits=2, space=3)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:40: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_local_clock("Human", "HowlerMon")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:46: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_alignment(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:52: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.optimise(show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:58: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_name("clock")
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:65: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    null_lnL = lf.get_log_likelihood()
    null_nfp = lf.get_num_free_params()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:72: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule("length", is_independent=True)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:78: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.optimise(show_progress=False)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:84: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_name("non clock")
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:91: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    LR = 2 * (lf.get_log_likelihood() - null_lnL)
    df = lf.get_num_free_params() - null_nfp
    P = stats.chisqprob(LR, df)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:99: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print("Likelihood ratio statistic = ", LR)
    print("degrees-of-freedom = ", df)
    print("probability = ", P)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:17: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, load_tree
    from cogent3.evolve.models import MG94HKY

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    tree = load_tree("data/test.tree")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:27: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    sm = MG94HKY()
    lf = sm.make_likelihood_function(tree, digits=2, space=3)
    lf.set_alignment(aln)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:35: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(tree.ascii_art())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule(
        "omega",
        tip_names=["DogFaced", "Mouse"],
        outgroup_name="Human",
        init=2.0,
        clade=True,
    )
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:73: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule("omega", init=1.0)
    lf.set_param_rule(
        "omega",
        tip_names=["Human", "HowlerMon"],
        outgroup_name="Mouse",
        init=2.0,
        stem=True,
        clade=False,
    )
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:91: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    lf.set_param_rule("omega", init=1.0)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:96: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule(
        "omega",
        tip_names=["Human", "HowlerMon"],
        outgroup_name="Mouse",
        init=2.0,
        stem=True,
        clade=True,
    )
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:160: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    lf.set_param_rule("omega", init=1.0)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:165: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule(
        "omega",
        tip_names=["Human", "HowlerMon"],
        outgroup_name="Mouse",
        clade=True,
        value=1.0,
        is_constant=True,
    )
    lf.optimise(local=True, show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:180: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule(
        "omega",
        tip_names=["Human", "HowlerMon"],
        outgroup_name="Mouse",
        clade=True,
        is_constant=False,
    )
    lf.optimise(local=True, show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:194: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule(
        "omega",
        tip_names=["Human", "HowlerMon"],
        outgroup_name="Mouse",
        clade=True,
        is_independent=True,
    )
    lf.optimise(local=True, show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/scope_model_params_on_trees.rst:208: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf.set_param_rule("omega", is_independent=True)
    lf.optimise(local=True, show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:14: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import DNA

    s = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig")
    exon1 = s.add_feature("exon", "exon1", [(10, 15)])
    exon2 = s.add_feature("exon", "exon2", [(30, 40)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:26: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.core.annotation import Feature

    s2 = DNA.make_seq("aagaagaagacccccaaaaaaaaaattttttttttaaaaaaaaaaaaa", name="Orig2")
    exon3 = s2.add_annotation(Feature, "exon", "exon1", [(35, 40)])
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:35: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    s[exon1]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:41: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    exons = s.get_annotations_matching("exon")
    print(exons)
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:48: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(s.get_region_covering_all(exons))
    s.get_region_covering_all(exons).get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:55: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    print(s.get_region_covering_all(exons).get_shadow().get_slice())
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:63: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    exon1[0:3].get_slice()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/simple.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/simple.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3.evolve.models import get_model
    from cogent3 import load_aligned_seqs, make_tree

    model = get_model("HKY85")
    aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta")
    tree = make_tree(tip_names=aln.names)
    lf = model.make_likelihood_function(tree)
    lf.set_alignment(aln)
    lf.optimise(show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/simulate_alignment.rst:8: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    import sys
    from cogent3 import make_tree
    from cogent3.evolve.models import get_model
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/simulate_alignment.rst:16: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);")
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/simulate_alignment.rst:22: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    sm = get_model("F81")
    lf = sm.make_likelihood_function(t)
    lf.set_constant_lengths()
    lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4))
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/simulate_alignment.rst:32: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    simulated = lf.simulate_alignment(sequence_length=1000)
    simulated
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:1: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::
    :hide-code:

    import set_working_directory
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:13: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    from cogent3 import load_aligned_seqs, make_tree, make_table
    from cogent3.evolve.models import HKY85
    from cogent3.recalculation.scope import EACH, ALL
    from cogent3.maths.stats import chisqprob

    aln = load_aligned_seqs("data/long_testseqs.fasta")
    half = len(aln) // 2
    aln1 = aln[:half]
    aln2 = aln[half:]
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:27: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    loci_names = ["1st-half", "2nd-half"]
    loci = [aln1, aln2]
    tree = make_tree(tip_names=aln.names)
    mod = HKY85()
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:36: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3)
    lf.set_param_rule("length", is_independent=False)
    lf.set_param_rule("kappa", loci=ALL)
    lf.set_alignment(loci)
    lf.optimise(show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:45: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    all_lnL = lf.lnL
    all_nfp = lf.nfp
    lf.set_param_rule("kappa", loci=EACH)
    lf.optimise(show_progress=False)
    lf
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:53: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    each_lnL = lf.lnL
    each_nfp = lf.nfp
    LR = 2 * (each_lnL - all_lnL)
    df = each_nfp - all_nfp
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/examples/testing_multi_loci.rst:62: WARNING: Unknown directive type "jupyter-execute".

.. jupyter-execute::

    make_table(
        header=["LR", "df", "p"], rows=[[LR, df, chisqprob(LR, df)]], digits=2, space=3,
    )
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/index.rst:8: WARNING: Unknown directive type "dropdown".

.. dropdown:: Click to see an animation showing testing a hypothesis involving a non-stationary nucleotide process.

    .. raw:: html

        <object type="image/gif" data="../_static/gif/demo-fit-ns.gif" style="height: 400px; width: auto;"></object>
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/index.rst:16: WARNING: Unknown directive type "dropdown".

.. dropdown:: Click to see an animation showing defining and using sequence annotations.

    .. raw:: html

        <object type="image/gif" data="../_static/gif/demo-annotate.gif" style="height: 400px; width: auto;"></object>
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/index.rst:22: WARNING: Unknown directive type "panels".

.. panels::
    :header: bg-primary
    :footer: text-right

    ---

    ``cogent3`` apps
    ^^^^^^^^^^^^^^^^

    ``cogent3`` comes with pre-defined "apps" that simplify otherwise complex tasks. They provide capabilities that can be used by themselves, or added together to define a pipeline. They also simplify parallel execution of pipelines.

    +++++++++++

    .. link-button:: app/index
        :type: ref
        :text: …
        :classes: stretched-link

    ---

    Cookbook
    ^^^^^^^^

    The cookbook presents short code recipes targeted at specific problems.

    +++++++++++

    .. link-button:: cookbook/index
        :type: ref
        :text: …
        :classes: stretched-link

    ---

    Tutorials
    ^^^^^^^^^

    The tutorials present code for solving more extensive problems.

    +++++++++++

    .. link-button:: examples/index
        :type: ref
        :text: …
        :classes: stretched-link

    ---

    API
    ^^^

    The API for major ``cogent3`` objects

    +++++++++++

    .. link-button:: api/index
        :type: ref
        :text: …
        :classes: stretched-link
looking for now-outdated files... none found
pickling environment... done
checking consistency... /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/data_file_links.rst: WARNING: document isn't included in any toctree
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/general.rst: WARNING: document isn't included in any toctree
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/install.rst: WARNING: document isn't included in any toctree
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/licenses.rst: WARNING: document isn't included in any toctree
/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc/pycogent.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  0%] api/__init__/cogent3.__init__.available_apps
writing output... [  1%] api/__init__/cogent3.__init__.available_codes
writing output... [  2%] api/__init__/cogent3.__init__.available_models
writing output... [  3%] api/__init__/cogent3.__init__.available_moltypes
writing output... [  4%] api/__init__/cogent3.__init__.get_code
writing output... [  5%] api/__init__/cogent3.__init__.get_model
writing output... [  6%] api/__init__/cogent3.__init__.get_moltype
writing output... [  7%] api/__init__/cogent3.__init__.load_aligned_seqs
writing output... [  8%] api/__init__/cogent3.__init__.load_delimited
writing output... [  9%] api/__init__/cogent3.__init__.load_table
writing output... [ 10%] api/__init__/cogent3.__init__.load_tree
writing output... [ 10%] api/__init__/cogent3.__init__.load_unaligned_seqs
writing output... [ 11%] api/__init__/cogent3.__init__.make_aligned_seqs
writing output... [ 12%] api/__init__/cogent3.__init__.make_seq
writing output... [ 13%] api/__init__/cogent3.__init__.make_table
writing output... [ 14%] api/__init__/cogent3.__init__.make_tree
writing output... [ 15%] api/__init__/cogent3.__init__.make_unaligned_seqs
writing output... [ 16%] api/alignment/alignment
writing output... [ 17%] api/alignment/classes/cogent3.core.alignment.Alignment
writing output... [ 18%] api/alignment/classes/cogent3.core.alignment.ArrayAlignment
writing output... [ 19%] api/alignment/classes/cogent3.core.alignment.SequenceCollection
writing output... [ 20%] api/alphabet/alphabet
writing output... [ 20%] api/alphabet/classes/cogent3.core.alphabet.Alphabet
writing output... [ 21%] api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode
writing output... [ 22%] api/genetic_code/genetic_code
writing output... [ 23%] api/index
writing output... [ 24%] api/moltype/classes/cogent3.core.moltype.MolType
writing output... [ 25%] api/moltype/moltype
writing output... [ 26%] api/sequence/classes/cogent3.core.sequence.DnaSequence
writing output... [ 27%] api/sequence/classes/cogent3.core.sequence.ProteinSequence
writing output... [ 28%] api/sequence/classes/cogent3.core.sequence.RnaSequence
writing output... [ 29%] api/sequence/sequence
writing output... [ 30%] api/table/classes/cogent3.parse.table.FilteringParser
writing output... [ 30%] api/table/classes/cogent3.util.table.Columns
writing output... [ 31%] api/table/classes/cogent3.util.table.Table
writing output... [ 32%] api/table/table
writing output... [ 33%] api/tree/classes/cogent3.core.tree.PhyloNode
writing output... [ 34%] api/tree/tree
writing output... [ 35%] app/align-codon
writing output... [ 36%] app/align-nucleotide
writing output... [ 37%] app/align-protein
writing output... [ 38%] app/app-overview
writing output... [ 39%] app/available-apps
writing output... [ 40%] app/dstore
writing output... [ 40%] app/evo-ancestral-states
writing output... [ 41%] app/evo-dt-nuc-model
writing output... [ 42%] app/evo-extract-model-stats
writing output... [ 43%] app/evo-hypothesis
writing output... [ 44%] app/evo-model
writing output... [ 45%] app/evo-model-timehet
writing output... [ 46%] app/evo-model-with-tree
writing output... [ 47%] app/evo-natsel_neutral
writing output... [ 48%] app/evo-natsel_sitehet
writing output... [ 49%] app/evo-natsel_timehet
writing output... [ 50%] app/evo-natsel_zhang
writing output... [ 50%] app/evo-nstat-codon-model
writing output... [ 51%] app/evo-tr-codon-model
writing output... [ 52%] app/evo-tr-nuc-model
writing output... [ 53%] app/index
writing output... [ 54%] app/not-completed
writing output... [ 55%] app/user_function
writing output... [ 56%] app/warning
writing output... [ 57%] cookbook/DNA_and_RNA_sequences
writing output... [ 58%] cookbook/alignments
writing output... [ 59%] cookbook/alphabet
writing output... [ 60%] cookbook/annotations
writing output... [ 60%] cookbook/building_alignments
writing output... [ 61%] cookbook/building_phylogenies
writing output... [ 62%] cookbook/calc_genetic_distance
writing output... [ 63%] cookbook/evo_modelling
writing output... [ 64%] cookbook/genetic_code
writing output... [ 65%] cookbook/index
writing output... [ 66%] cookbook/loading_sequences
writing output... [ 67%] cookbook/loading_tabular
writing output... [ 68%] cookbook/manipulating_biological_data
writing output... [ 69%] cookbook/moltypes
writing output... [ 70%] cookbook/protein_sequences
writing output... [ 70%] cookbook/simple_trees
writing output... [ 71%] cookbook/tables
writing output... [ 72%] cookbook/useful_utilities
writing output... [ 73%] cookbook/what_codes
writing output... [ 74%] data_file_links
writing output... [ 75%] examples/align_codons_to_protein
writing output... [ 76%] examples/calculate_UPGMA_cluster
writing output... [ 77%] examples/calculate_neigbourjoining_tree
writing output... [ 78%] examples/calculate_pairwise_distances
writing output... [ 79%] examples/codon_models
writing output... [ 80%] examples/coevolution
writing output... [ 80%] examples/complete_seq_features
writing output... [ 81%] examples/empirical_protein_models
writing output... [ 82%] examples/hmm_par_heterogeneity
writing output... [ 83%] examples/index
writing output... [ 84%] examples/manipulating_tree_nodes
writing output... [ 85%] examples/neutral_test
writing output... [ 86%] examples/parallel
writing output... [ 87%] examples/parametric_bootstrap
writing output... [ 88%] examples/period_estimation
writing output... [ 89%] examples/phylo_by_ls
writing output... [ 90%] examples/rate_heterogeneity
writing output... [ 90%] examples/relative_rate
writing output... [ 91%] examples/scope_model_params_on_trees
writing output... [ 92%] examples/seq_features
writing output... [ 93%] examples/simple
writing output... [ 94%] examples/simulate_alignment
writing output... [ 95%] examples/testing_multi_loci
writing output... [ 96%] general
writing output... [ 97%] index
writing output... [ 98%] install
writing output... [ 99%] licenses
writing output... [100%] pycogent

generating indices... genindex done
writing additional pages... search done
copying downloadable files... [  4%] data/abglobin_aa.phylip
copying downloadable files... [  8%] data/dists_for_phylo.json
copying downloadable files... [ 12%] data/long_testseqs.fasta
copying downloadable files... [ 16%] data/primate_brca1.fasta
copying downloadable files... [ 20%] data/primate_brca1.tree
copying downloadable files... [ 24%] data/primate_cdx2_promoter.fasta
copying downloadable files... [ 28%] data/test.paml
copying downloadable files... [ 32%] data/test.tree
copying downloadable files... [ 36%] data/test2.fasta
copying downloadable files... [ 40%] data/trna_profile.fasta
copying downloadable files... [ 44%] data/refseqs.fasta
copying downloadable files... [ 48%] data/refseqs_protein.fasta
copying downloadable files... [ 52%] data/inseqs.fasta
copying downloadable files... [ 56%] data/inseqs_protein.fasta
copying downloadable files... [ 60%] data/SCA1-cds.fasta
copying downloadable files... [ 64%] data/tp53.json
copying downloadable files... [ 68%] data/brca1-bats.fasta
copying downloadable files... [ 72%] data/brca1.fasta
copying downloadable files... [ 76%] data/GN-tree.json
copying downloadable files... [ 80%] data/tree-with-support.json
copying downloadable files... [ 84%] data/F9-demo.fa
copying downloadable files... [ 88%] data/BRCA1-demo.fasta
copying downloadable files... [ 92%] data/tbp.jaspar
copying downloadable files... [ 96%] data/stats.tsv
copying downloadable files... [100%] data/CerebellumDukeDNaseSeq.pk

copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 858 warnings.

The HTML pages are in _build/html.

Build finished. The HTML pages are in _build/html.
rm -rf draw/
make[2]: Leaving directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/doc'
# remove superfluous files and dirs
find doc/_build -name "*.doctree*" -delete
rm -f doc/_build/html/_sources/COGENT_LICENSE.txt
rm -f doc/_build/html/_static/jquery.js
rm -f doc/_build/html/_static/underscore.js
rm -rf doc/_build/html/_images/math/
make[1]: Leaving directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
   dh_auto_test -a -O--buildsystem=pybuild
I: pybuild pybuild:285: cp -r /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/tests/data /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build
I: pybuild base:232: cd /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build; python3.9 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip'
============================= test session starts ==============================
platform linux -- Python 3.9.7, pytest-6.2.5, py-1.10.0, pluggy-0.13.0
rootdir: /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg, configfile: pyproject.toml
collected 2605 items / 5 deselected / 2600 selected

tests/test_phylo.py ................                                     [  0%]
tests/test_recalculation.py .                                            [  0%]
tests/test_align/test_align.py .............................             [  1%]
tests/test_app/test_align.py .......................                     [  2%]
tests/test_app/test_app_mpi.py s                                         [  2%]
tests/test_app/test_composable.py ......................                 [  3%]
tests/test_app/test_data_store.py .............ss.............s......... [  5%]
...........                                                              [  5%]
tests/test_app/test_dist.py ......                                       [  5%]
tests/test_app/test_evo.py .......................................       [  7%]
tests/test_app/test_init.py ...                                          [  7%]
tests/test_app/test_io.py .............................                  [  8%]
tests/test_app/test_result.py ...........................                [  9%]
tests/test_app/test_sample.py ................                           [ 10%]
tests/test_app/test_translate.py ......                                  [ 10%]
tests/test_app/test_tree.py .....                                        [ 10%]
tests/test_cluster/test_UPGMA.py .......                                 [ 10%]
tests/test_core/test_alignment.py ...................................... [ 12%]
........................................................................ [ 14%]
........................................................................ [ 17%]
........................................................................ [ 20%]
........................................................................ [ 23%]
.............................................................            [ 25%]
tests/test_core/test_alphabet.py ............................            [ 26%]
tests/test_core/test_annotation.py .........                             [ 27%]
tests/test_core/test_core_standalone.py ................................ [ 28%]
.........................                                                [ 29%]
tests/test_core/test_features.py .............................           [ 30%]
tests/test_core/test_genetic_code.py ...................                 [ 31%]
tests/test_core/test_info.py ............                                [ 31%]
tests/test_core/test_location.py ...................................     [ 32%]
tests/test_core/test_maps.py ....                                        [ 33%]
tests/test_core/test_moltype.py ........................................ [ 34%]
.........................                                                [ 35%]
tests/test_core/test_profile.py ................................         [ 36%]
tests/test_core/test_seq_aln_integration.py ..............               [ 37%]
tests/test_core/test_sequence.py ....................................... [ 38%]
........................................................................ [ 41%]
........................................................................ [ 44%]
.............................                                            [ 45%]
tests/test_core/test_tree.py ........................................... [ 47%]
........................................................................ [ 49%]
.......................                                                  [ 50%]
tests/test_data/test_molecular_weight.py .                               [ 50%]
tests/test_draw/test_dendrogram.py .........                             [ 51%]
tests/test_draw/test_dotplot.py ...........                              [ 51%]
tests/test_draw/test_draw_integration.py ......................          [ 52%]
tests/test_draw/test_logo.py .....                                       [ 52%]
tests/test_draw/test_shapes.py ...                                       [ 52%]
tests/test_evolve/test_best_likelihood.py .......                        [ 53%]
tests/test_evolve/test_bootstrap.py ..                                   [ 53%]
tests/test_evolve/test_coevolution.py .................................. [ 54%]
........................................................................ [ 57%]
..............                                                           [ 57%]
tests/test_evolve/test_distance.py ..................................... [ 59%]
.....                                                                    [ 59%]
tests/test_evolve/test_likelihood_function.py .......................... [ 60%]
.........................................                                [ 61%]
tests/test_evolve/test_models.py ...........                             [ 62%]
tests/test_evolve/test_motifchange.py .............                      [ 62%]
tests/test_evolve/test_newq.py .............                             [ 63%]
tests/test_evolve/test_ns_substitution_model.py ..............           [ 63%]
tests/test_evolve/test_parameter_controller.py ..........                [ 64%]
tests/test_evolve/test_scale_rules.py ....                               [ 64%]
tests/test_evolve/test_substitution_model.py ......................      [ 65%]
tests/test_format/test_bedgraph.py ........                              [ 65%]
tests/test_format/test_clustal.py ...                                    [ 65%]
tests/test_format/test_fasta.py .                                        [ 65%]
tests/test_maths/test_distance_transform.py ............................ [ 66%]
.....                                                                    [ 66%]
tests/test_maths/test_geometry.py ..........                             [ 67%]
tests/test_maths/test_matrix_exponential_integration.py ....             [ 67%]
tests/test_maths/test_matrix_logarithm.py ...                            [ 67%]
tests/test_maths/test_measure.py .......                                 [ 67%]
tests/test_maths/test_optimisers.py ......                               [ 68%]
tests/test_maths/test_period.py .......                                  [ 68%]
tests/test_maths/test_util.py .......                                    [ 68%]
tests/test_maths/test_stats/test_contingency.py ....................     [ 69%]
tests/test_maths/test_stats/test_distribution.py ....................... [ 70%]
..............                                                           [ 70%]
tests/test_maths/test_stats/test_information_criteria.py ...             [ 70%]
tests/test_maths/test_stats/test_jackknife.py ....                       [ 71%]
tests/test_maths/test_stats/test_ks.py ......                            [ 71%]
tests/test_maths/test_stats/test_number.py ......................        [ 72%]
tests/test_maths/test_stats/test_period.py ..........                    [ 72%]
tests/test_maths/test_stats/test_special.py .......................      [ 73%]
tests/test_maths/test_stats/test_test.py ............................... [ 74%]
........................................................................ [ 77%]
                                                                         [ 77%]
tests/test_parse/test_blast.py ..............                            [ 77%]
tests/test_parse/test_blast_xml.py ...............                       [ 78%]
tests/test_parse/test_cigar.py .....                                     [ 78%]
tests/test_parse/test_clustal.py .........                               [ 79%]
tests/test_parse/test_dialign.py ...                                     [ 79%]
tests/test_parse/test_ebi.py ........................................... [ 80%]
............                                                             [ 81%]
tests/test_parse/test_fasta.py .....................                     [ 82%]
tests/test_parse/test_gbseq.py .                                         [ 82%]
tests/test_parse/test_genbank.py ................                        [ 82%]
tests/test_parse/test_gff.py ......                                      [ 83%]
tests/test_parse/test_greengenes.py ....                                 [ 83%]
tests/test_parse/test_locuslink.py .............                         [ 83%]
tests/test_parse/test_ncbi_taxonomy.py ..................                [ 84%]
tests/test_parse/test_nexus.py ...............                           [ 84%]
tests/test_parse/test_pamlmatrix.py .                                    [ 84%]
tests/test_parse/test_phylip.py ...                                      [ 85%]
tests/test_parse/test_psl.py ...                                         [ 85%]
tests/test_parse/test_pwm_parsers.py ..                                  [ 85%]
tests/test_parse/test_rdb.py ..................                          [ 85%]
tests/test_parse/test_record.py ........................................ [ 87%]
..                                                                       [ 87%]
tests/test_parse/test_record_finder.py .................                 [ 88%]
tests/test_parse/test_tinyseq.py .                                       [ 88%]
tests/test_parse/test_tree.py ...............                            [ 88%]
tests/test_parse/test_unigene.py ....                                    [ 89%]
tests/test_util/test_deserialise.py ..........................           [ 90%]
tests/test_util/test_dictarray.py ...............................        [ 91%]
tests/test_util/test_misc.py ........................................... [ 92%]
...................................................                      [ 94%]
tests/test_util/test_parallel.py ..s.                                    [ 94%]
tests/test_util/test_recode_alignment.py ...............                 [ 95%]
tests/test_util/test_table.py .......................................... [ 97%]
..........................................................               [ 99%]
tests/test_util/test_transform.py .....                                  [ 99%]
tests/test_util/test_union_dict.py ...........                           [100%]

=============================== warnings summary ===============================
.pybuild/cpython3_3.9_cogent3/build/tests/test_app/test_data_store.py::TinyDBDataStoreTests::test_db_creation
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py:946: UserWarning: 'tmpyc7_nmpg/data.tinydb' is locked to 606196, current pid is 606196.
    warn(f"'{self.source}' is locked to {locked_id}, current pid is {pid}.")

.pybuild/cpython3_3.9_cogent3/build/tests/test_app/test_data_store.py::TinyDBDataStoreTests::test_db_creation2
  /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function ReadOnlyTinyDbDataStore.__del__ at 0x7a5a5ae3af70>
  
  Traceback (most recent call last):
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 681, in __del__
      self.close()
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 695, in close
      self.unlock()
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 721, in unlock
      got = self.db.get(query)
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 668, in db
      self._db = TinyDB(self.source, storage=storage)
    File "/usr/lib/python3/dist-packages/tinydb/database.py", line 159, in __init__
      self._storage = storage(*args, **kwargs)
    File "/usr/lib/python3/dist-packages/tinydb/middlewares.py", line 63, in __call__
      self.storage = self._storage_cls(*args, **kwargs)
    File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 99, in __init__
      touch(path, create_dirs=create_dirs)  # Create file if not exists
    File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 34, in touch
      with open(fname, 'a'):
  FileNotFoundError: [Errno 2] No such file or directory: 'tmpi2uufn3z/subdir/data.tinydb'
  
    warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))

.pybuild/cpython3_3.9_cogent3/build/tests/test_app/test_evo.py::TestModel::test_hyp_init
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/evo.py:316: UserWarning: init_alt is specified, ignoring sequential
    warnings.warn("init_alt is specified, ignoring sequential")

.pybuild/cpython3_3.9_cogent3/build/tests/test_app/test_evo.py::TestHypothesisResult::test_alt_hyp_fail_error
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/core/sequence.py:1117: UserWarning: Dropped remainder "GA" from end of sequence
    warnings.warn(

.pybuild/cpython3_3.9_cogent3/build/tests/test_app/test_evo.py::TestBootstrap::test_bstrap
  /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function ReadOnlyTinyDbDataStore.__del__ at 0x7a5a5ae3af70>
  
  Traceback (most recent call last):
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 681, in __del__
      self.close()
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 695, in close
      self.unlock()
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 721, in unlock
      got = self.db.get(query)
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 668, in db
      self._db = TinyDB(self.source, storage=storage)
    File "/usr/lib/python3/dist-packages/tinydb/database.py", line 159, in __init__
      self._storage = storage(*args, **kwargs)
    File "/usr/lib/python3/dist-packages/tinydb/middlewares.py", line 63, in __call__
      self.storage = self._storage_cls(*args, **kwargs)
    File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 99, in __init__
      touch(path, create_dirs=create_dirs)  # Create file if not exists
    File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 34, in touch
      with open(fname, 'a'):
  FileNotFoundError: [Errno 2] No such file or directory: 'tmpdp7xqkp_/delme.tinydb'
  
    warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))

.pybuild/cpython3_3.9_cogent3/build/tests/test_app/test_io.py::TestIo::test_load_tabular
  /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: <function ReadOnlyTinyDbDataStore.__del__ at 0x7a5a5ae3af70>
  
  Traceback (most recent call last):
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 681, in __del__
      self.close()
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 695, in close
      self.unlock()
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 721, in unlock
      got = self.db.get(query)
    File "/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/app/data_store.py", line 668, in db
      self._db = TinyDB(self.source, storage=storage)
    File "/usr/lib/python3/dist-packages/tinydb/database.py", line 159, in __init__
      self._storage = storage(*args, **kwargs)
    File "/usr/lib/python3/dist-packages/tinydb/middlewares.py", line 63, in __call__
      self.storage = self._storage_cls(*args, **kwargs)
    File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 99, in __init__
      touch(path, create_dirs=create_dirs)  # Create file if not exists
    File "/usr/lib/python3/dist-packages/tinydb/storages.py", line 34, in touch
      with open(fname, 'a'):
  FileNotFoundError: [Errno 2] No such file or directory: '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/tests/tmp026dyg_m/delme.tinydb'
  
    warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))

.pybuild/cpython3_3.9_cogent3/build/tests/test_core/test_alignment.py::SequenceCollectionTests::test_get_identical_sets
.pybuild/cpython3_3.9_cogent3/build/tests/test_core/test_alignment.py::AlignmentTests::test_get_identical_sets
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/core/alignment.py:890: UserWarning: in get_identical_sets, mask_degen has no effect as moltype 'text' has no degenerate characters
    warnings.warn(

.pybuild/cpython3_3.9_cogent3/build/tests/test_core/test_alignment.py::ArrayAlignmentTests::test_get_identical_sets
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/core/alignment.py:4240: UserWarning: in get_identical_sets, mask_degen has no effect as moltype 'text' has no degenerate characters
    warnings.warn(

.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_likelihood_function.py::LikelihoodFunctionTests::test_make_discrete_markov
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_likelihood_function.py:785: UserWarning: Ignoring tree edge lengths
    lf = dm.make_likelihood_function(t)

.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_cond_pos_differ
.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_get_motif_probs
.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_get_statistics
.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_newQ_is_nuc_process
.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_results_different
.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_newq.py::NewQ::test_sim_alignment
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/evolve/substitution_model.py:721: UserWarning: Motif probs overspecified
    _ContinuousSubstitutionModel.__init__(self, alphabet, **kw)

.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/maths/optimisers.py:192: UserWarning: Unused arg for local alignment: results
    warnings.warn("Unused arg for local alignment: " + k)

.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_ns_substitution_model.py::NonStatMarkov::test_general_vs_constructed_general
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/tests/test_evolve/test_ns_substitution_model.py:125: UserWarning: FORCED EXIT from optimiser after 25 evaluations
    nuc_lf.optimise(**optargs)

.pybuild/cpython3_3.9_cogent3/build/tests/test_maths/test_stats/test_test.py::TestsTests::test_median
.pybuild/cpython3_3.9_cogent3/build/tests/test_maths/test_stats/test_test.py::TestsTests::test_median
.pybuild/cpython3_3.9_cogent3/build/tests/test_maths/test_stats/test_test.py::TestsTests::test_median
.pybuild/cpython3_3.9_cogent3/build/tests/test_maths/test_stats/test_test.py::TestsTests::test_median
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/maths/stats/test.py:161: DeprecationWarning: function median is discontinued, support will be stopped in version 2021.11
    discontinued("function", "median", "2021.11")

.pybuild/cpython3_3.9_cogent3/build/tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch
  /usr/lib/python3/dist-packages/numpy/core/_methods.py:233: RuntimeWarning: Degrees of freedom <= 0 for slice
    ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,

.pybuild/cpython3_3.9_cogent3/build/tests/test_util/test_misc.py::UtilsTests::test_get_setting_from_environ
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3/util/misc.py:1268: UserWarning: could not cast name=blah to type <class 'float'>, skipping
    warnings.warn(

.pybuild/cpython3_3.9_cogent3/build/tests/test_util/test_table.py::TableTests::test_cast_str_to_numerical
  /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/tests/test_util/test_table.py:1773: ComplexWarning: Casting complex values to real discards the imaginary part
    d = d.astype(d_type)

-- Docs: https://docs.pytest.org/en/stable/warnings.html
==== 2595 passed, 5 skipped, 5 deselected, 25 warnings in 238.88s (0:03:58) ====
   create-stamp debian/debhelper-build-stamp
   dh_testroot -a -O--buildsystem=pybuild
   dh_prep -a -O--buildsystem=pybuild
   dh_auto_install -a -O--buildsystem=pybuild
I: pybuild plugin_flit:66: Installing package /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/src/cogent3 -> /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/debian/python3-cogent3/usr/lib/python3.9/dist-packages/cogent3
I: pybuild plugin_flit:79: Writing dist-info /build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg/debian/python3-cogent3/usr/lib/python3.9/dist-packages
   dh_install -a -O--buildsystem=pybuild
   debian/rules override_dh_installdocs
make[1]: Entering directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
dh_installdocs
rm -rf debian/python-cogent/usr/share/doc/python-cogent/html/_sources
find debian -name doctrees -type d | xargs rm -rf
make[1]: Leaving directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
   dh_installchangelogs -a -O--buildsystem=pybuild
   debian/rules override_dh_python3
make[1]: Entering directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
dh_python3 --shebang=/usr/bin/python3
I: dh_python3 pydist:235: Cannot find package that provides jupyterlab. Please add package that provides it to Build-Depends or add "jupyterlab python3-jupyterlab" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
I: dh_python3 pydist:235: Cannot find package that provides jupytext. Please add package that provides it to Build-Depends or add "jupytext python3-jupytext" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
I: dh_python3 pydist:235: Cannot find package that provides kaleido. Please add package that provides it to Build-Depends or add "kaleido python3-kaleido" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
I: dh_python3 pydist:235: Cannot find package that provides sphinx_panels. Please add package that provides it to Build-Depends or add "sphinx_panels python3-sphinx-panels" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
I: dh_python3 pydist:235: Cannot find package that provides jupyterlab. Please add package that provides it to Build-Depends or add "jupyterlab python3-jupyterlab" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
I: dh_python3 pydist:235: Cannot find package that provides jupytext. Please add package that provides it to Build-Depends or add "jupytext python3-jupytext" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
I: dh_python3 pydist:235: Cannot find package that provides kaleido. Please add package that provides it to Build-Depends or add "kaleido python3-kaleido" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
I: dh_python3 pydist:235: Cannot find package that provides sphinx_panels. Please add package that provides it to Build-Depends or add "sphinx_panels python3-sphinx-panels" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
I: dh_python3 pydist:235: Cannot find package that provides kaleido. Please add package that provides it to Build-Depends or add "kaleido python3-kaleido" line to debian/py3dist-overrides or add proper dependency to Depends by hand and ignore this info.
make[1]: Leaving directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
   dh_installsystemduser -a -O--buildsystem=pybuild
   dh_lintian -a -O--buildsystem=pybuild
   dh_perl -a -O--buildsystem=pybuild
   dh_link -a -O--buildsystem=pybuild
   dh_strip_nondeterminism -a -O--buildsystem=pybuild
   debian/rules override_dh_compress
make[1]: Entering directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb
make[1]: Leaving directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
   dh_fixperms -a -O--buildsystem=pybuild
   dh_missing -a -O--buildsystem=pybuild
   dh_dwz -a -O--buildsystem=pybuild
   dh_strip -a -O--buildsystem=pybuild
   dh_makeshlibs -a -O--buildsystem=pybuild
   debian/rules override_dh_shlibdeps
make[1]: Entering directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
dh_shlibdeps
dh_numpy3
make[1]: Leaving directory '/build/python-cogent-yPSVqR/python-cogent-2021.10.12a1+dfsg'
   dh_installdeb -a -O--buildsystem=pybuild
   dh_gencontrol -a -O--buildsystem=pybuild
dpkg-gencontrol: warning: Depends field of package python3-cogent3: substitution variable ${shlibs:Depends} used, but is not defined
   dh_md5sums -a -O--buildsystem=pybuild
   dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python3-cogent3' in '../python3-cogent3_2021.10.12a1+dfsg-1_amd64.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any >../python-cogent_2021.10.12a1+dfsg-1_amd64.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
I: running special hook: sync-out /build/python-cogent-yPSVqR /tmp/python-cogent-2021.10.12a1+dfsg-1c54l8p6r
I: cleaning package lists and apt cache...
I: creating tarball...
I: done
I: removing tempdir /tmp/mmdebstrap.PMfnIfpgYp...
I: success in 3456.5169 seconds
md5: Value of 'md5' differs for python3-cogent3_2021.10.12a1+dfsg-1_amd64.deb
md5: Size differs for python3-cogent3_2021.10.12a1+dfsg-1_amd64.deb
sha1: Value of 'sha1' differs for python3-cogent3_2021.10.12a1+dfsg-1_amd64.deb
sha1: Size differs for python3-cogent3_2021.10.12a1+dfsg-1_amd64.deb
sha256: Value of 'sha256' differs for python3-cogent3_2021.10.12a1+dfsg-1_amd64.deb
sha256: Size differs for python3-cogent3_2021.10.12a1+dfsg-1_amd64.deb
Checksums: FAIL
diffoscope run passed