https://launchpad.net/ubuntu/+source/python-cogent/2021.10.12a1+dfsg-1/+build/22372250 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-012 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:39:40 UTC 2021 s390x Buildd toolchain package versions: launchpad-buildd_203~505~ubuntu18.04.1 python3-lpbuildd_203~505~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 4 Nov 17:36:47 ntpdate[1738]: adjust time server 10.211.37.1 offset 0.000025 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22372250 --image-type chroot /home/buildd/filecache-default/63391afefe2c3c1f68eb13dcf1e745f5d0398db6 Creating target for build PACKAGEBUILD-22372250 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22372250 Starting target for build PACKAGEBUILD-22372250 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22372250 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22372250 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22372250 Updating target for build PACKAGEBUILD-22372250 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [254 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [105 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main s390x Packages [1336 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe s390x Packages [13.0 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5506 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x Packages [345 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [117 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x Packages [1665 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [809 kB] Fetched 23.8 MB in 7s (3413 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bsdutils ca-certificates cpp-11 dash debconf debianutils e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libblkid1 libcc1-0 libcom-err2 libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libisl23 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libseccomp2 libselinux1 libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libtasn1-6 libtinfo6 libubsan1 libuuid1 libzstd1 lockfile-progs logsave make mount ncurses-base ncurses-bin pkgbinarymangler sensible-utils tzdata usrmerge util-linux 72 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 160 MB of archives. After this operation, 400 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x bsdutils s390x 1:2.37.2-4ubuntu1 [81.0 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x debianutils s390x 5.5-1 [77.5 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x debconf all 1.5.79 [126 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x dash s390x 0.5.11+git20210903+057cd650a4ed-3 [92.2 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x grep s390x 3.7-1 [156 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libncursesw6 s390x 6.2+20210905-1 [142 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libncurses6 s390x 6.2+20210905-1 [109 kB] Get:8 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libtinfo6 s390x 6.2+20210905-1 [105 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x ncurses-bin s390x 6.2+20210905-1 [182 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libblkid1 s390x 2.37.2-4ubuntu1 [100 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libselinux1 s390x 3.1-3build3 [74.2 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libmount1 s390x 2.37.2-4ubuntu1 [119 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x util-linux s390x 2.37.2-4ubuntu1 [1055 kB] Get:14 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x ncurses-base all 6.2+20210905-1 [19.9 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libcc1-0 s390x 11.2.0-10ubuntu1 [52.8 kB] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gcc-11-base s390x 11.2.0-10ubuntu1 [21.0 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgcc-s1 s390x 11.2.0-10ubuntu1 [28.4 kB] Get:18 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgomp1 s390x 11.2.0-10ubuntu1 [113 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libitm1 s390x 11.2.0-10ubuntu1 [29.7 kB] Get:20 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libatomic1 s390x 11.2.0-10ubuntu1 [9018 B] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libasan6 s390x 11.2.0-10ubuntu1 [2247 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libubsan1 s390x 11.2.0-10ubuntu1 [911 kB] Get:23 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x g++-11 s390x 11.2.0-10ubuntu1 [47.7 MB] Get:24 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libstdc++-11-dev s390x 11.2.0-10ubuntu1 [2078 kB] Get:25 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgcc-11-dev s390x 11.2.0-10ubuntu1 [829 kB] Get:26 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gcc-11 s390x 11.2.0-10ubuntu1 [49.8 MB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x cpp-11 s390x 11.2.0-10ubuntu1 [43.2 MB] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libstdc++6 s390x 11.2.0-10ubuntu1 [689 kB] Get:29 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libisl23 s390x 0.24-2 [699 kB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libmpc3 s390x 1.2.1-1 [47.6 kB] Get:31 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libzstd1 s390x 1.4.8+dfsg-3 [317 kB] Get:32 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgpg-error0 s390x 1.42-3 [67.6 kB] Get:33 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgcrypt20 s390x 1.9.4-3ubuntu2 [457 kB] Get:34 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libapt-pkg6.0 s390x 2.3.11 [869 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gpgv s390x 2.2.27-2ubuntu1 [133 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main s390x libidn2-0 s390x 2.3.2-2 [66.3 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main s390x libp11-kit0 s390x 0.24.0-5 [258 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main s390x libtasn1-6 s390x 4.17.0-2 [43.9 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgnutls30 s390x 3.7.2-2ubuntu1 [867 kB] Get:40 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libseccomp2 s390x 2.5.1-1ubuntu2 [47.9 kB] Get:41 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x apt s390x 2.3.11 [1366 kB] Get:42 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libpam0g s390x 1.4.0-10ubuntu1 [60.2 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libpam-modules-bin s390x 1.4.0-10ubuntu1 [40.2 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libpam-modules s390x 1.4.0-10ubuntu1 [279 kB] Get:45 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x logsave s390x 1.46.4-1ubuntu1 [10.8 kB] Get:46 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libext2fs2 s390x 1.46.4-1ubuntu1 [210 kB] Get:47 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x e2fsprogs s390x 1.46.4-1ubuntu1 [582 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x mount s390x 2.37.2-4ubuntu1 [113 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libattr1 s390x 1:2.5.1-1 [13.3 kB] Get:50 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libcom-err2 s390x 1.46.4-1ubuntu1 [9948 B] Get:51 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libk5crypto3 s390x 1.18.3-7 [88.3 kB] Get:52 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libkrb5support0 s390x 1.18.3-7 [32.2 kB] Get:53 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libkrb5-3 s390x 1.18.3-7 [347 kB] Get:54 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libgssapi-krb5-2 s390x 1.18.3-7 [138 kB] Get:55 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libpam-runtime all 1.4.0-10ubuntu1 [40.2 kB] Get:56 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsmartcols1 s390x 2.37.2-4ubuntu1 [50.0 kB] Get:57 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libuuid1 s390x 2.37.2-4ubuntu1 [23.9 kB] Get:58 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libss2 s390x 1.46.4-1ubuntu1 [12.1 kB] Get:59 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x sensible-utils all 0.0.17 [20.1 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main s390x usrmerge all 25ubuntu2 [54.7 kB] Get:61 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x ca-certificates all 20211016 [148 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main s390x libapparmor1 s390x 3.0.3-0ubuntu2 [37.3 kB] Get:63 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x libsqlite3-0 s390x 3.36.0-2 [630 kB] Get:64 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x tzdata all 2021e-1ubuntu1 [343 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main s390x libgdbm6 s390x 1.22-1 [35.3 kB] Get:66 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gpg s390x 2.2.27-2ubuntu1 [505 kB] Get:67 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gpgconf s390x 2.2.27-2ubuntu1 [94.0 kB] Get:68 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x gpg-agent s390x 2.2.27-2ubuntu1 [206 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main s390x libgdbm-compat4 s390x 1.22-1 [6554 B] Get:70 http://ftpmaster.internal/ubuntu jammy/main s390x lockfile-progs s390x 0.1.19 [9654 B] Get:71 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x make s390x 4.3-4ubuntu2 [181 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main s390x pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 160 MB in 6s (25.0 MB/s) (Reading database ... 13030 files and directories currently installed.) 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Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 13019 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.4.0-10ubuntu1_s390x.deb ... Unpacking libpam-modules-bin (1.4.0-10ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam-modules-bin (1.4.0-10ubuntu1) ... (Reading database ... 13017 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.4.0-10ubuntu1_s390x.deb ... Unpacking libpam-modules:s390x (1.4.0-10ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam-modules:s390x (1.4.0-10ubuntu1) ... Installing new version of config file /etc/security/namespace.conf ... Installing new version of config file /etc/security/pam_env.conf ... (Reading database ... 13018 files and directories currently installed.) Preparing to unpack .../logsave_1.46.4-1ubuntu1_s390x.deb ... Unpacking logsave (1.46.4-1ubuntu1) over (1.46.3-1ubuntu3) ... 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Current default time zone: 'Etc/UTC' Local time is now: Thu Nov 4 17:37:18 UTC 2021. Universal Time is now: Thu Nov 4 17:37:18 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up make (4.3-4ubuntu2) ... Setting up libncurses6:s390x (6.2+20210905-1) ... Setting up libmpc3:s390x (1.2.1-1) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:s390x (11.2.0-10ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:s390x (1.46.4-1ubuntu1) ... Setting up libncursesw6:s390x (6.2+20210905-1) ... Setting up logsave (1.46.4-1ubuntu1) ... Setting up libubsan1:s390x (11.2.0-10ubuntu1) ... Setting up mount (2.37.2-4ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up gpgconf (2.2.27-2ubuntu1) ... Setting up libisl23:s390x (0.24-2) ... Setting up libcc1-0:s390x (11.2.0-10ubuntu1) ... Setting up gpg (2.2.27-2ubuntu1) ... Setting up libitm1:s390x (11.2.0-10ubuntu1) ... Setting up libgdbm6:s390x (1.22-1) ... Setting up cpp-11 (11.2.0-10ubuntu1) ... Setting up gpg-agent (2.2.27-2ubuntu1) ... Setting up pkgbinarymangler (149) ... Setting up e2fsprogs (1.46.4-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libgdbm-compat4:s390x (1.22-1) ... Setting up libgcc-11-dev:s390x (11.2.0-10ubuntu1) ... Setting up gcc-11 (11.2.0-10ubuntu1) ... Setting up libstdc++-11-dev:s390x (11.2.0-10ubuntu1) ... Setting up g++-11 (11.2.0-10ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22372250 s390x jammy-proposed -c chroot:build-PACKAGEBUILD-22372250 --arch=s390x --dist=jammy-proposed --nolog python-cogent_2021.10.12a1+dfsg-1.dsc Initiating build PACKAGEBUILD-22372250 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-161-generic #169-Ubuntu SMP Fri Oct 15 13:39:40 UTC 2021 s390x sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-s390x-012.buildd +==============================================================================+ | python-cogent 2021.10.12a1+dfsg-1 (s390x) Thu, 04 Nov 2021 17:37:22 +0000 | +==============================================================================+ Package: python-cogent Version: 2021.10.12a1+dfsg-1 Source Version: 2021.10.12a1+dfsg-1 Distribution: jammy-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22372250/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-cogent_2021.10.12a1+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-cogent-wXf8de/python-cogent-2021.10.12a1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/python-cogent-wXf8de' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-CzVBF5/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-CzVBF5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CzVBF5/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-CzVBF5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CzVBF5/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-CzVBF5/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-CzVBF5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13029 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, flit, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest, cython3, pandoc Filtered Build-Depends: debhelper-compat (= 13), dh-python, flit, python3-all-dev, python3-matplotlib, python3-numba, python3-numpy, python3-pandas, python3-scitrack, python3-tqdm, python3-tinydb, python3-sphinx, python3-numpydoc, python3-nbsphinx, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-pytest, cython3, pandoc dpkg-deb: building package 'sbuild-build-depends-python-cogent-dummy' in '/<>/resolver-CzVBF5/apt_archive/sbuild-build-depends-python-cogent-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-python-cogent-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-CzVBF5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-CzVBF5/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-CzVBF5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-CzVBF5/apt_archive ./ Sources [614 B] Get:5 copy:/<>/resolver-CzVBF5/apt_archive ./ Packages [680 B] Fetched 2257 B in 0s (0 B/s) Reading package lists... Reading package lists... Install python-cogent build dependencies (apt-based resolver) ------------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binfmt-support black bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fonts-lyx gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcmark-gfm-extensions0 libcmark-gfm0 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu67 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libllvm9 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenjp2-7 libpfm4 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libraqm0 libsigsegv2 libsub-override-perl libtbb2 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 llvm-9 llvm-9-runtime m4 mailcap man-db media-types mime-support pandoc pandoc-data po-debconf python-babel-localedata python-matplotlib-data python-pip-whl python3 python3-alabaster python3-all python3-all-dev python3-appdirs python3-attr python3-babel python3-bleach python3-certifi python3-chardet python3-click python3-colorama python3-cov-core python3-coverage python3-cycler python3-dateutil python3-decorator python3-defusedxml python3-dev python3-distlib python3-distutils python3-docutils python3-entrypoints python3-filelock python3-html5lib python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-ipython-genutils python3-isort python3-jinja2 python3-jsonschema python3-jupyter-core python3-kiwisolver python3-lib2to3 python3-llvmlite python3-markupsafe python3-matplotlib python3-minimal python3-mistune python3-more-itertools python3-mypy-extensions python3-nbconvert python3-nbformat python3-nbsphinx python3-nose2 python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pathspec python3-pil python3-pip python3-pkg-resources python3-platformdirs python3-pluggy python3-py python3-pygments python3-pyparsing python3-pyrsistent python3-pytest python3-pytest-cov python3-pytoml python3-regex python3-requests python3-roman python3-scipy python3-scitrack python3-setuptools python3-six python3-snowballstemmer python3-sphinx python3-sphinx-bootstrap-theme python3-sphinx-gallery python3-testpath python3-tinydb python3-toml python3-tqdm python3-traitlets python3-tz python3-urllib3 python3-virtualenv python3-webencodings python3-wheel python3-zipp python3.10 python3.10-dev python3.10-minimal python3.9 python3.9-dev python3.9-minimal sgml-base sphinx-common tox ttf-bitstream-vera xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python-black-doc cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libjs-jquery-ui-docs liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk llvm-9-doc m4-doc apparmor less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python ruby r-base-core libjs-mathjax node-katex citation-style-language-styles libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc python-bleach-doc python-coverage-doc python-cycler-doc docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base python3-genshi python3-lxml python-jinja2-doc python-jsonschema-doc llvmlite-doc dvipng ffmpeg ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt5 python3-sip python3-tornado texlive-extra-utils ttf-staypuft python-nbconvert-doc texlive-fonts-recommended texlive-plain-generic python-nbsphinx-doc python-nose2-doc gfortran python-numpy-doc python3-numpy-dbg python-pandas-doc python3-statsmodels python-pil-doc subversion python-pygments-doc python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc python-setuptools-doc python3-stemmer fonts-freefont-otf imagemagick-6.q16 latexmk python3-sphinx-rtd-theme sphinx-doc tex-gyre python-sphinx-gallery-doc python3-seaborn python3.10-venv python3.10-doc python3.9-venv python3.9-doc sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libltdl-dev llvm-9-dev libmail-sendmail-perl libpaper-utils python3-tk python3-jupyter-client python3-sphinxcontrib.bibtex numba-doc python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-bs4 python3-lxml python3-tables python3-olefile The following NEW packages will be installed: autoconf automake autopoint autotools-dev binfmt-support black bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dwz file flit fonts-lyx gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcmark-gfm-extensions0 libcmark-gfm0 libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu67 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-hotkeys libjs-jquery-isonscreen libjs-jquery-metadata libjs-jquery-tablesorter libjs-jquery-throttle-debounce libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libllvm9 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenjp2-7 libpfm4 libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libraqm0 libsigsegv2 libsub-override-perl libtbb2 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 libxml2 llvm-9 llvm-9-runtime m4 mailcap man-db media-types mime-support pandoc pandoc-data po-debconf python-babel-localedata python-matplotlib-data python-pip-whl python3 python3-alabaster python3-all python3-all-dev python3-appdirs python3-attr python3-babel python3-bleach python3-certifi python3-chardet python3-click python3-colorama python3-cov-core python3-coverage python3-cycler python3-dateutil python3-decorator python3-defusedxml python3-dev python3-distlib python3-distutils python3-docutils python3-entrypoints python3-filelock python3-html5lib python3-idna python3-imagesize python3-importlib-metadata python3-iniconfig python3-ipython-genutils python3-isort python3-jinja2 python3-jsonschema python3-jupyter-core python3-kiwisolver python3-lib2to3 python3-llvmlite python3-markupsafe python3-matplotlib python3-minimal python3-mistune python3-more-itertools python3-mypy-extensions python3-nbconvert python3-nbformat python3-nbsphinx python3-nose2 python3-numba python3-numpy python3-numpydoc python3-packaging python3-pandas python3-pandas-lib python3-pandocfilters python3-pathspec python3-pil python3-pip python3-pkg-resources python3-platformdirs python3-pluggy python3-py python3-pygments python3-pyparsing python3-pyrsistent python3-pytest python3-pytest-cov python3-pytoml python3-regex python3-requests python3-roman python3-scipy python3-scitrack python3-setuptools python3-six python3-snowballstemmer python3-sphinx python3-sphinx-bootstrap-theme python3-sphinx-gallery python3-testpath python3-tinydb python3-toml python3-tqdm python3-traitlets python3-tz python3-urllib3 python3-virtualenv python3-webencodings python3-wheel python3-zipp python3.10 python3.10-dev python3.10-minimal python3.9 python3.9-dev python3.9-minimal sbuild-build-depends-python-cogent-dummy sgml-base sphinx-common tox ttf-bitstream-vera xml-core zlib1g-dev 0 upgraded, 207 newly installed, 0 to remove and 0 not upgraded. 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jammy-proposed/main s390x python3-pil s390x 8.3.2-1 [432 kB] Get:176 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x python3-matplotlib s390x 3.3.4-2 [6324 kB] Get:177 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-mistune all 0.8.4-5 [14.6 kB] Get:178 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-nbformat all 5.1.3-1 [31.4 kB] Get:179 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-pandocfilters all 1.4.3-1 [20.1 kB] Get:180 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-testpath all 0.5.0+dfsg-1 [9900 B] Get:181 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-nbconvert all 5.6.1-3 [341 kB] Get:182 http://ftpmaster.internal/ubuntu jammy-proposed/main s390x sphinx-common all 4.2.0-5 [672 kB] Get:183 http://ftpmaster.internal/ubuntu jammy/main s390x python3-alabaster all 0.7.12-1 [17.8 kB] Get:184 http://ftpmaster.internal/ubuntu jammy/main s390x python3-snowballstemmer all 2.1.0-2 [60.7 kB] Get:185 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jammy/universe s390x python3-pip all 20.3.4-4 [283 kB] Get:195 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-platformdirs all 2.4.0-1 [13.4 kB] Get:196 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x python3-pluggy all 0.13.0-7.1 [19.0 kB] Get:197 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-py all 1.10.0-1 [71.9 kB] Get:198 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x python3-pytest all 6.2.5-1ubuntu1 [214 kB] Get:199 http://ftpmaster.internal/ubuntu jammy/universe s390x libjs-jquery-isonscreen all 1.2.0-1.1 [3244 B] Get:200 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x python3-pytest-cov all 3.0.0-1 [21.0 kB] Get:201 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x python3-virtualenv all 20.10.0+ds-1 [73.5 kB] Get:202 http://ftpmaster.internal/ubuntu jammy/universe s390x tox all 3.21.4-1 [251 kB] Get:203 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x python3-scitrack all 2021.5.3-1 [9226 B] Get:204 http://ftpmaster.internal/ubuntu jammy-proposed/universe s390x python3-sphinx-bootstrap-theme all 0.8.0-1 [430 kB] Get:205 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-sphinx-gallery all 0.10.0-1 [94.8 kB] Get:206 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-tinydb all 3.15.2-2 [16.2 kB] Get:207 http://ftpmaster.internal/ubuntu jammy/universe s390x python3-tqdm all 4.57.0-2 [93.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 176 MB in 10s (18.4 MB/s) Selecting previously unselected package libpython3.9-minimal:s390x. 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Unpacking python3-tqdm (4.57.0-2) ... Selecting previously unselected package sbuild-build-depends-python-cogent-dummy. Preparing to unpack .../195-sbuild-build-depends-python-cogent-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-python-cogent-dummy (0.invalid.0) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:s390x (1.5.3-1build1) ... Setting up libgraphite2-3:s390x (1.3.14-1build1) ... Setting up liblcms2-2:s390x (2.12~rc1-2build1) ... Setting up libxau6:s390x (1:1.0.9-1build4) ... Setting up ttf-bitstream-vera (1.10-8.1) ... Setting up bsdextrautils (2.37.2-4ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:s390x (67.1-7ubuntu1) ... Setting up libmagic-mgc (1:5.39-3build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:s390x (2.70.0-3) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.3.4ubuntu3) ... Setting up libbrotli1:s390x (1.0.9-2build4) ... Setting up libtbb2:s390x (2020.3-1) ... Setting up libmagic1:s390x (1:5.39-3build1) ... Setting up libdeflate0:s390x (1.7-2ubuntu2) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up file (1:5.39-3build1) ... Setting up libjs-jquery-throttle-debounce (1.1+dfsg.1-1.1) ... Setting up libjbig0:s390x (2.1-3.1build2) ... Setting up python-babel-localedata (2.8.0+dfsg.1-7) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:s390x (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Setting up libpfm4:s390x (4.11.1+git32-gd0b85fb-1) ... Setting up libexpat1-dev:s390x (2.4.1-3) ... Setting up libfreetype6:s390x (2.11.0+dfsg-1) ... Setting up libsigsegv2:s390x (2.13-1ubuntu2) ... Setting up libfribidi0:s390x (1.0.8-2ubuntu2) ... Setting up libimagequant0:s390x (2.12.2-1.1build1) ... Setting up libpython3.10-minimal:s390x (3.10.0-3) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up binfmt-support (2.2.1-1) ... Created symlink /etc/systemd/system/multi-user.target.wants/binfmt-support.service → /lib/systemd/system/binfmt-support.service. Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libwebp6:s390x (0.6.1-2.1build1) ... Setting up libcmark-gfm0:s390x (0.29.0.gfm.0-6) ... Setting up libjpeg-turbo8:s390x (2.0.6-0ubuntu3) ... Setting up libgfortran5:s390x (11.2.0-10ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-2ubuntu7) ... Setting up libmd0:s390x (1.0.4-1) ... Setting up libuchardet0:s390x (0.0.7-1build1) ... Setting up libmpdec3:s390x (2.5.1-2build1) ... Setting up libopenjp2-7:s390x (2.4.0-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:s390x (2.7.4-1ubuntu2) ... Setting up sgml-base (1.30) ... Setting up python-pip-whl (20.3.4-4) ... Setting up pandoc-data (2.9.2.1-1ubuntu4) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-8) ... Setting up libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2ubuntu1) ... Setting up python-matplotlib-data (3.3.4-2) ... Setting up libwebpmux3:s390x (0.6.1-2.1build1) ... Setting up libbsd0:s390x (0.11.3-1ubuntu3) ... Setting up mailcap (3.70ubuntu1) ... Setting up libelf1:s390x (0.185-2) ... Setting up libxml2:s390x (2.9.12+dfsg-5) ... Setting up libpython3.9-stdlib:s390x (3.9.7-4) ... Setting up libpython3-stdlib:s390x (3.9.4-1ubuntu2) ... Setting up libjs-underscore (1.9.1~dfsg-4) ... Setting up libjpeg8:s390x (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.12.0-2) ... Setting up libdw1:s390x (0.185-2) ... Setting up libxdmcp6:s390x (1:1.1.3-0ubuntu4) ... Setting up liblapack3:s390x (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode Setting up libxcb1:s390x (1.14-3ubuntu2) ... Setting up gettext (0.21-4ubuntu3) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15build1) ... Setting up libwebpdemux2:s390x (0.6.1-2.1build1) ... Setting up libedit2:s390x (3.1-20210910-1) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up python3.10-minimal (3.10.0-3) ... Setting up libcmark-gfm-extensions0:s390x (0.29.0.gfm.0-6) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3.10-stdlib:s390x (3.10.0-3) ... Setting up libpython3.9:s390x (3.9.7-4) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8) ... Setting up pandoc (2.9.2.1-1ubuntu4) ... Setting up libjs-jquery-metadata (12-3) ... Setting up libraqm0:s390x (0.7.0-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libjs-sphinxdoc (4.2.0-5) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up dwz (0.14-1build1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-2) ... Setting up groff-base (1.22.4-7) ... Setting up xml-core (0.18+nmu1) ... Setting up debugedit (1:5.0-0ubuntu2) ... Setting up libtiff5:s390x (4.3.0-2) ... Setting up libllvm9:s390x (1:9.0.1-16.1ubuntu1) ... Setting up python3.9 (3.9.7-4) ... Setting up liblbfgsb0:s390x (3.0+dfsg.3-9) ... Setting up automake (1:1.16.5-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.10:s390x (3.10.0-3) ... Setting up python3.10 (3.10.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.9-dev:s390x (3.9.7-4) ... Setting up python3 (3.9.4-1ubuntu2) ... Setting up python3-distlib (0.3.2+really+0.3.1-0.1) ... Setting up python3-pandocfilters (1.4.3-1) ... Setting up man-db (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-markupsafe (2.0.1-2) ... Setting up python3-wheel (0.34.2-1) ... Setting up python3-webencodings (0.5.1-4) ... Setting up python3-platformdirs (2.4.0-1) ... Setting up python3-tz (2021.3-1) ... Setting up python3-six (1.16.0-2) ... Setting up dh-autoreconf (20) ... Setting up python3-pil:s390x (8.3.2-1) ... Setting up python3-roman (3.3-1) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-certifi (2020.6.20-1) ... Setting up python3-sphinx-bootstrap-theme (0.8.0-1) ... Setting up python3-snowballstemmer (2.1.0-2) ... Setting up python3-testpath (0.5.0+dfsg-1) ... Setting up sphinx-common (4.2.0-5) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.3.2-1) ... Setting up python3-idna (2.10-1) ... Setting up cython3 (0.29.24-0ubuntu3) ... Setting up libpython3.10-dev:s390x (3.10.0-3) ... Setting up llvm-9-runtime (1:9.0.1-16.1ubuntu1) ... Setting up python3-regex (0.1.20211008-1) ... Setting up python3-html5lib (1.1-3) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-isort (5.6.4-1) ... Setting up python3-urllib3 (1.26.5-1~exp1) ... Setting up python3.10-dev (3.10.0-3) ... Setting up python3-pyrsistent:s390x (0.15.5-1build5) ... Setting up python3.9-dev (3.9.7-4) ... Setting up python3-traitlets (5.1.1-1) ... Setting up python3-pytoml (0.1.21-1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up python3-pathspec (0.9.0-1) ... Setting up python3-lib2to3 (3.9.7-1) ... Setting up python3-appdirs (1.4.4-1) ... Setting up python3-mistune (0.8.4-5) ... Setting up python3-imagesize (1.2.0-2) ... Setting up python3-pkg-resources (58.2.0-1) ... Setting up python3-entrypoints (0.3-8) ... Setting up python3-distutils (3.9.7-1) ... Setting up dh-python (5.20211022.1) ... Setting up python3-more-itertools (4.2.0-3) ... Setting up python3-iniconfig (1.1.1-1) ... Setting up python3-attr (20.3.0-1) ... Setting up python3-filelock (3.3.2-1) ... Setting up libpython3-dev:s390x (3.9.4-1ubuntu2) ... Setting up python3-setuptools (58.2.0-1) ... Setting up python3-py (1.10.0-1) ... Setting up python3-babel (2.8.0+dfsg.1-7) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-colorama (0.4.4-1) ... Setting up python3-defusedxml (0.7.1-1) ... Setting up python3-ipython-genutils (0.2.0-5) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-mypy-extensions (0.4.3-2) ... Setting up python3-tqdm (4.57.0-2) ... Setting up python3-tinydb (3.15.2-2) ... Setting up python3-all (3.9.4-1ubuntu2) ... Setting up python3-coverage (5.1+dfsg.1-2build2) ... Setting up debhelper (13.3.4ubuntu3) ... Setting up python3-nose2 (0.9.2-1) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-click (8.0.2-1) ... Setting up python3-jinja2 (3.0.1-2) ... Setting up python3-pygments (2.7.1+dfsg-2.1) ... Setting up python3-packaging (21.0-1) ... Setting up python3-chardet (4.0.0-1) ... Setting up llvm-9 (1:9.0.1-16.1ubuntu1) ... Setting up libpython3-all-dev:s390x (3.9.4-1ubuntu2) ... Setting up python3-dev (3.9.4-1ubuntu2) ... Setting up python3-requests (2.25.1+dfsg-2) ... Setting up python3-pip (20.3.4-4) ... Setting up python3-numpy (1:1.20.2-1ubuntu1) ... Setting up python3-jupyter-core (4.9.1-1) ... Setting up python3-all-dev (3.9.4-1ubuntu2) ... Setting up python3-matplotlib (3.3.4-2) ... Setting up python3-scipy (1.7.1-1ubuntu1) ... Setting up python3-importlib-metadata (4.6.4-1) ... Setting up python3-cov-core (1.15.0-3build1) ... Setting up python3-pandas-lib:s390x (1.1.5+dfsg-2ubuntu1) ... Setting up python3-virtualenv (20.10.0+ds-1) ... Setting up black (21.4b2-3) ... Setting up python3-bleach (4.1.0-1) ... Setting up python3-llvmlite (0.35.0-3build1) ... Setting up python3-pandas (1.1.5+dfsg-2ubuntu1) ... Setting up python3-jsonschema (3.2.0-0ubuntu2) ... Setting up python3-pluggy (0.13.0-7.1) ... Setting up tox (3.21.4-1) ... Setting up python3-pytest (6.2.5-1ubuntu1) ... Setting up python3-pytest-cov (3.0.0-1) ... Setting up python3-nbformat (5.1.3-1) ... Setting up python3-numba (0.52.0-4) ... update-alternatives: using /usr/share/python3-numba/numba to provide /usr/bin/numba (numba) in auto mode Setting up python3-nbconvert (5.6.1-3) ... Setting up python3-scitrack (2021.5.3-1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for sgml-base (1.30) ... Setting up docutils-common (0.17.1+dfsg-2) ... Processing triggers for sgml-base (1.30) ... Setting up python3-docutils (0.17.1+dfsg-2) ... Setting up flit (3.0.0-1) ... Setting up python3-sphinx (4.2.0-5) ... Setting up python3-sphinx-gallery (0.10.0-1) ... Setting up python3-nbsphinx (0.8.7+ds-1) ... Setting up python3-numpydoc (1.1.0-3) ... Setting up sbuild-build-depends-python-cogent-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-161-generic s390x (s390x) Toolchain package versions: binutils_2.37-7ubuntu1 dpkg-dev_1.20.9ubuntu2 g++-11_11.2.0-10ubuntu1 gcc-11_11.2.0-10ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-10ubuntu1 libstdc++6_11.2.0-10ubuntu1 linux-libc-dev_5.13.0-19.19 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu1 base-passwd_3.5.52 bash_5.1-3ubuntu2 binfmt-support_2.2.1-1 binutils_2.37-7ubuntu1 binutils-common_2.37-7ubuntu1 binutils-s390x-linux-gnu_2.37-7ubuntu1 black_21.4b2-3 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-4ubuntu4 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libapparmor1_3.0.3-0ubuntu2 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build22 libasan6_11.2.0-10ubuntu1 libassuan0_2.5.5-1 libatomic1_11.2.0-10ubuntu1 libattr1_1:2.5.1-1 libaudit-common_1:3.0-2ubuntu3 libaudit1_1:3.0-2ubuntu3 libbinutils_2.37-7ubuntu1 libblas3_3.9.0-3ubuntu3 libblkid1_2.37.2-4ubuntu1 libbrotli1_1.0.9-2build4 libbsd0_0.11.3-1ubuntu3 libbz2-1.0_1.0.8-4ubuntu4 libc-bin_2.34-0ubuntu3 libc-dev-bin_2.34-0ubuntu3 libc6_2.34-0ubuntu3 libc6-dev_2.34-0ubuntu3 libcap-ng0_0.7.9-2.2build2 libcap2_1:2.44-1build2 libcc1-0_11.2.0-10ubuntu1 libcmark-gfm-extensions0_0.29.0.gfm.0-6 libcmark-gfm0_0.29.0.gfm.0-6 libcom-err2_1.46.4-1ubuntu1 libcrypt-dev_1:4.4.18-4ubuntu2 libcrypt1_1:4.4.18-4ubuntu2 libcryptsetup12_2:2.3.6-0ubuntu1 libctf-nobfd0_2.37-7ubuntu1 libctf0_2.37-7ubuntu1 libdb5.3_5.3.28+dfsg1-0.8ubuntu2 libdebconfclient0_0.256ubuntu4 libdebhelper-perl_13.3.4ubuntu3 libdeflate0_1.7-2ubuntu2 libdevmapper1.02.1_2:1.02.175-2.1ubuntu3 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python3-entrypoints_0.3-8 python3-filelock_3.3.2-1 python3-html5lib_1.1-3 python3-idna_2.10-1 python3-imagesize_1.2.0-2 python3-importlib-metadata_4.6.4-1 python3-iniconfig_1.1.1-1 python3-ipython-genutils_0.2.0-5 python3-isort_5.6.4-1 python3-jinja2_3.0.1-2 python3-jsonschema_3.2.0-0ubuntu2 python3-jupyter-core_4.9.1-1 python3-kiwisolver_1.3.2-1 python3-lib2to3_3.9.7-1 python3-llvmlite_0.35.0-3build1 python3-markupsafe_2.0.1-2 python3-matplotlib_3.3.4-2 python3-minimal_3.9.4-1ubuntu2 python3-mistune_0.8.4-5 python3-more-itertools_4.2.0-3 python3-mypy-extensions_0.4.3-2 python3-nbconvert_5.6.1-3 python3-nbformat_5.1.3-1 python3-nbsphinx_0.8.7+ds-1 python3-nose2_0.9.2-1 python3-numba_0.52.0-4 python3-numpy_1:1.20.2-1ubuntu1 python3-numpydoc_1.1.0-3 python3-packaging_21.0-1 python3-pandas_1.1.5+dfsg-2ubuntu1 python3-pandas-lib_1.1.5+dfsg-2ubuntu1 python3-pandocfilters_1.4.3-1 python3-pathspec_0.9.0-1 python3-pil_8.3.2-1 python3-pip_20.3.4-4 python3-pkg-resources_58.2.0-1 python3-platformdirs_2.4.0-1 python3-pluggy_0.13.0-7.1 python3-py_1.10.0-1 python3-pygments_2.7.1+dfsg-2.1 python3-pyparsing_2.4.7-1 python3-pyrsistent_0.15.5-1build5 python3-pytest_6.2.5-1ubuntu1 python3-pytest-cov_3.0.0-1 python3-pytoml_0.1.21-1 python3-regex_0.1.20211008-1 python3-requests_2.25.1+dfsg-2 python3-roman_3.3-1 python3-scipy_1.7.1-1ubuntu1 python3-scitrack_2021.5.3-1 python3-setuptools_58.2.0-1 python3-six_1.16.0-2 python3-snowballstemmer_2.1.0-2 python3-sphinx_4.2.0-5 python3-sphinx-bootstrap-theme_0.8.0-1 python3-sphinx-gallery_0.10.0-1 python3-testpath_0.5.0+dfsg-1 python3-tinydb_3.15.2-2 python3-toml_0.10.2-1 python3-tqdm_4.57.0-2 python3-traitlets_5.1.1-1 python3-tz_2021.3-1 python3-urllib3_1.26.5-1~exp1 python3-virtualenv_20.10.0+ds-1 python3-webencodings_0.5.1-4 python3-wheel_0.34.2-1 python3-zipp_1.0.0-3 python3.10_3.10.0-3 python3.10-dev_3.10.0-3 python3.10-minimal_3.10.0-3 python3.9_3.9.7-4 python3.9-dev_3.9.7-4 python3.9-minimal_3.9.7-4 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-python-cogent-dummy_0.invalid.0 sed_4.7-1ubuntu2 sensible-utils_0.0.17 sgml-base_1.30 sphinx-common_4.2.0-5 systemd_248.3-1ubuntu8 systemd-sysv_248.3-1ubuntu8 systemd-timesyncd_248.3-1ubuntu8 sysvinit-utils_2.96-7ubuntu2 tar_1.34+dfsg-1build2 tox_3.21.4-1 ttf-bitstream-vera_1.10-8.1 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 xml-core_0.18+nmu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Nov 4 08:55:42 2021 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-cogent_2021.10.12a1+dfsg-1.dsc dpkg-source: info: extracting python-cogent in /<>/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 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-22372250 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22372250 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22372250 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2021.10.12a1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x 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 '/<>/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 '/<>/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 '/<>/python-cogent-2021.10.12a1+dfsg' dh_auto_build W: pybuild validate:120: Couldn't get list of valid classifiers to check against I: pybuild plugin_flit:66: Installing package /<>/python-cogent-2021.10.12a1+dfsg/src/cogent3 -> /<>/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.10_cogent3/build/cogent3 I: pybuild plugin_flit:79: Writing dist-info /<>/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.10_cogent3/build/ W: pybuild validate:120: Couldn't get list of valid classifiers to check against I: pybuild plugin_flit:66: Installing package /<>/python-cogent-2021.10.12a1+dfsg/src/cogent3 -> /<>/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/cogent3 I: pybuild plugin_flit:79: Writing dist-info /<>/python-cogent-2021.10.12a1+dfsg/.pybuild/cpython3_3.9_cogent3/build/ set -x; cd doc; PYTHONPATH=/<>/python-cogent-2021.10.12a1+dfsg http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/<>/python-cogent-2021.10.12a1+dfsg http_proxy=127.0.0.1:9 /usr/bin/make html make[2]: Entering directory '/<>/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 /<>/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 ----- /<>/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. /<>/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 ----- /<>/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. /<>/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 /<>/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") /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:33: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/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 /<>/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 /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/align-codon.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/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 /<>/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") /<>/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 /<>/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 /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/align-nucleotide.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/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 /<>/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") /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/align-protein.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned.info /<>/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() /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /<>/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:41: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /<>/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:50: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.tail() /<>/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:57: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.filtered("*ENSG00000067704*") /<>/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) /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:92: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /<>/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:101: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /<>/python-cogent-2021.10.12a1+dfsg/doc/app/dstore.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /<>/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 /<>/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 /<>/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) /<>/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 /<>/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"] /<>/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) /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-dt-nuc-model.rst:27: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/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) /<>/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 /<>/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"] /<>/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 /<>/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) /<>/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 /<>/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"] /<>/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"] /<>/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"] /<>/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 /<>/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") /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:31: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:56: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-hypothesis.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/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 /<>/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 /<>/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 /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:49: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:55: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:59: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:69: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment /<>/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") /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model.rst:95: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] /<>/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 /<>/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) /<>/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")], ) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-timehet.rst:50: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-model-with-tree.rst:51: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /<>/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 /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:26: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_neutral.rst:30: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_sitehet.rst:29: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/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] /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_timehet.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/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 /<>/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=' 1', '0 < omega0 < 1'], dtype='>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-natsel_zhang.rst:48: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /<>/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] /<>/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 /<>/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 /<>/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 /<>/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") /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-nstat-codon-model.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/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) /<>/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 /<>/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") /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-codon-model.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/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 /<>/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") /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/app/evo-tr-nuc-model.rst:34: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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] /<>/python-cogent-2021.10.12a1+dfsg/doc/app/user_function.rst:36: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: up_to /<>/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 /<>/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 /<>/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 /<>/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 /<>/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) /<>/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") /<>/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()) /<>/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() /<>/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) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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) /<>/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] /<>/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" /<>/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" /<>/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()) /<>/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 /<>/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)) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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() /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:169: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names aln.names /<>/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]) /<>/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 /<>/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")) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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)) /<>/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") /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alignments.rst:302: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") /<>/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) /<>/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 /<>/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) /<>/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() /<>/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]) /<>/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]) /<>/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] /<>/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] /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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", ) /<>/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) /<>/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) /<>/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]) /<>/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]) /<>/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]) /<>/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]) /<>/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"]) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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])) /<>/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 /<>/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 /<>/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") /<>/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]) /<>/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)) /<>/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) /<>/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] /<>/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] /<>/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] /<>/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] /<>/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)) /<>/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)) /<>/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) /<>/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()) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/alphabet.rst:20: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN /<>/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) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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) /<>/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) /<>/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) /<>/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") /<>/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)]) /<>/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)]) /<>/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)]) /<>/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]) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:143: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds.get_coordinates() /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:159: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: cds /<>/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)]) /<>/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)] ) /<>/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] /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:209: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s1[exon2] exon2.get_slice() /<>/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]) /<>/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]) /<>/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] /<>/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()) /<>/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]) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/annotations.rst:272: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ValueError aln1[seq_exon] /<>/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 /<>/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() /<>/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 /<>/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 /<>/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]) /<>/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] /<>/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] /<>/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]) /<>/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]) /<>/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]) /<>/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]) /<>/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="?")) /<>/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="?")) /<>/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)) /<>/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 /<>/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() /<>/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 /<>/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)]) /<>/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) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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) /<>/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()) /<>/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") /<>/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 /<>/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 /<>/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()) /<>/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) /<>/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()) /<>/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()) /<>/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()) /<>/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) /<>/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) /<>/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 /<>/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() /<>/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 /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/calc_genetic_distance.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr /<>/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 /<>/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 /<>/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() /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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()) /<>/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, ) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:134: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:321: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:326: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:338: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/evo_modelling.rst:353: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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}") /<>/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] /<>/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}") /<>/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 /<>/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 /<>/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) /<>/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] /<>/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] /<>/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") /<>/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) /<>/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] /<>/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"] /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/genetic_code.rst:51: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /<>/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"] /<>/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"] /<>/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 /<>/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()) /<>/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) /<>/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() /<>/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)) /<>/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()) /<>/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 /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_sequences.rst:25: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /<>/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) /<>/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 /<>/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) /<>/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) /<>/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) /<>/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 /<>/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 /<>/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 /<>/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)) /<>/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) /<>/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 /<>/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 /<>/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 /<>/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] /<>/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] /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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")) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:141: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] /<>/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 /<>/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 /<>/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 /<>/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"] /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/loading_tabular.rst:190: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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() /<>/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") /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:53: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/moltypes.rst:60: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") /<>/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 /<>/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") /<>/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 /<>/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 /<>/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 /<>/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) /<>/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") /<>/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") /<>/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 /<>/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()) /<>/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") /<>/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] /<>/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"] /<>/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") /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:63: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:79: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) /<>/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) /<>/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) /<>/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()) /<>/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) /<>/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() /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:154: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) /<>/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) /<>/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) /<>/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() /<>/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]) /<>/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() /<>/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) /<>/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()) /<>/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()) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:247: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) /<>/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()) /<>/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()) /<>/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() /<>/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) /<>/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) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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) /<>/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()) /<>/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()) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/simple_trees.rst:377: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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()) /<>/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) /<>/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()) /<>/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) /<>/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) /<>/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) /<>/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]) /<>/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) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/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"]) /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:91: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:107: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] /<>/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) /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:128: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] /<>/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] /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:165: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table /<>/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 /<>/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 /<>/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() /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:199: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:208: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:214: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) /<>/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 /<>/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 /<>/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) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:300: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /<>/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 /<>/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() /<>/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() /<>/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 /<>/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") /<>/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 /<>/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 /<>/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 /<>/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="") /<>/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 /<>/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 /<>/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") /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:414: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:434: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /<>/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) /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:458: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /<>/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) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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") /<>/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") /<>/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") /<>/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 /<>/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 /<>/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"]) /<>/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 /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:574: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:585: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /<>/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 /<>/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 /<>/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 /<>/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) /<>/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) /<>/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")) /<>/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")) /<>/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)) /<>/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()) /<>/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")) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/tables.rst:754: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /<>/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, ) ) /<>/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() /<>/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 /<>/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") /<>/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") /<>/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 /<>/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) /<>/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) /<>/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) /<>/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) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:100: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) /<>/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") /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:118: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:122: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) /<>/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]] /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:137: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:152: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:156: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") /<>/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) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:186: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:216: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:220: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:224: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:228: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:232: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:254: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:258: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:262: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/cookbook/useful_utilities.rst:278: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) /<>/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 /<>/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 /<>/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 /<>/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() /<>/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] /<>/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] /<>/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 /<>/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 /<>/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()) /<>/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()) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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") /<>/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) /<>/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()) /<>/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") /<>/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") /<>/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 /<>/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 /<>/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 /<>/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") /<>/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) /<>/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()) /<>/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") /<>/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") /<>/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 /<>/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 /<>/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 /<>/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") /<>/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() /<>/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") /<>/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) /<>/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) /<>/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 /<>/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 /<>/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") /<>/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") /<>/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) /<>/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 /<>/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 /<>/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)) /<>/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() /<>/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)) /<>/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() /<>/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") /<>/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 ) /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:164: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 /<>/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 ) /<>/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]) /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/codon_models.rst:195: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chisqprob(LR, df)) /<>/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() /<>/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=' 1', '0 < omega0 < 1'], dtype='>/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) /<>/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"])) /<>/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 ) /<>/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) /<>/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) /<>/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, ) /<>/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, ], ) /<>/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) /<>/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) /<>/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, ) /<>/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) /<>/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) /<>/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) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/coevolution.rst:76: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(coevolve_pair_functions.keys()) /<>/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) /<>/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)]) /<>/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() /<>/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) /<>/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] /<>/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()) /<>/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() /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/complete_seq_features.rst:54: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1, exon2] /<>/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] /<>/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] /<>/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() /<>/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) /<>/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]) /<>/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) /<>/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()) /<>/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") /<>/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) /<>/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()]) /<>/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) /<>/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]) /<>/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() /<>/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 /<>/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 /<>/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()) /<>/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()) /<>/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()) /<>/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()]) /<>/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)] /<>/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()) /<>/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) ) /<>/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)) /<>/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) /<>/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)]) /<>/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)]) /<>/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) /<>/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")) /<>/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 /<>/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 /<>/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) /<>/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") /<>/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") /<>/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) /<>/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) /<>/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 /<>/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 /<>/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 /<>/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") /<>/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) /<>/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 /<>/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 /<>/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 /<>/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) /<>/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 /<>/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)) /<>/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)) /<>/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() /<>/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]) /<>/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") /<>/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 ) /<>/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" ) /<>/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 /<>/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 /<>/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) /<>/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()) /<>/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) /<>/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) /<>/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") /<>/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) /<>/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()) /<>/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()) /<>/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()) /<>/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] /<>/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)) /<>/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() /<>/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) /<>/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() /<>/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)) /<>/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 /<>/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 /<>/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") /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:40: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:52: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/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() /<>/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) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/neutral_test.rst:77: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /<>/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() /<>/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) /<>/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}") /<>/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 /<>/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 /<>/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) /<>/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 /<>/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") /<>/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 ) /<>/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) /<>/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) /<>/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() /<>/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()) /<>/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) /<>/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 /<>/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) /<>/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) /<>/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) /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:89: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) /<>/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 /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:117: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:130: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/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 /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:139: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /<>/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) /<>/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] /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/period_estimation.rst:172: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] /<>/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 /<>/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 /<>/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) /<>/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) /<>/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) /<>/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)) /<>/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 /<>/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 /<>/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) /<>/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 /<>/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) /<>/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) /<>/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()) /<>/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 /<>/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) /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/phylo_by_ls.rst:83: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) /<>/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] /<>/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()) /<>/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()) /<>/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)" ) /<>/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) /<>/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" /<>/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") /<>/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 /<>/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 /<>/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 /<>/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) /<>/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 /<>/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) /<>/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 /<>/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 /<>/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") /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:28: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") /<>/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) /<>/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") /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/relative_rate.rst:46: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) /<>/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) /<>/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 /<>/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() /<>/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) /<>/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) /<>/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 /<>/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) /<>/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) /<>/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 /<>/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") /<>/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) /<>/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()) /<>/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 /<>/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 /<>/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) /<>/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 /<>/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) /<>/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 /<>/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 /<>/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 /<>/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 /<>/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)]) /<>/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)]) /<>/python-cogent-2021.10.12a1+dfsg/doc/examples/seq_features.rst:35: WARNING: Unknown directive type "jupyter-execute". .. jupyter-execute:: s[exon1] /<>/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) /<>/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() /<>/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()) /<>/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() /<>/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 /<>/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 /<>/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 /<>/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);") /<>/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 /<>/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 /<>/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 /<>/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:] /<>/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() /<>/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 /<>/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 /<>/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 /<>/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, ) /<>/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 /<>/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 /<>/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... /<>/python-cogent-2021.10.12a1+dfsg/doc/data_file_links.rst: WARNING: document isn't included in any toctree /<>/python-cogent-2021.10.12a1+dfsg/doc/general.rst: WARNING: document isn't included in any toctree /<>/python-cogent-2021.10.12a1+dfsg/doc/install.rst: WARNING: document isn't included in any toctree /<>/python-cogent-2021.10.12a1+dfsg/doc/licenses.rst: WARNING: document isn't included in any toctree /<>/python-cogent-2021.10.12a1+dfsg/doc/pycogent.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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[ 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 '/<>/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 '/<>/python-cogent-2021.10.12a1+dfsg' dh_auto_test -a -O--buildsystem=pybuild 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 W: pybuild validate:120: Couldn't get list of valid classifiers to check against I: pybuild plugin_flit:66: Installing package /<>/python-cogent-2021.10.12a1+dfsg/src/cogent3 -> /<>/python-cogent-2021.10.12a1+dfsg/debian/python3-cogent3/usr/lib/python3.10/dist-packages/cogent3 I: pybuild plugin_flit:79: Writing dist-info /<>/python-cogent-2021.10.12a1+dfsg/debian/python3-cogent3/usr/lib/python3.10/dist-packages W: pybuild validate:120: Couldn't get list of valid classifiers to check against I: pybuild plugin_flit:66: Installing package /<>/python-cogent-2021.10.12a1+dfsg/src/cogent3 -> /<>/python-cogent-2021.10.12a1+dfsg/debian/python3-cogent3/usr/lib/python3.9/dist-packages/cogent3 I: pybuild plugin_flit:79: Writing dist-info /<>/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 '/<>/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 '/<>/python-cogent-2021.10.12a1+dfsg' dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/<>/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 '/<>/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 '/<>/python-cogent-2021.10.12a1+dfsg' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/<>/python-cogent-2021.10.12a1+dfsg' dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -a -O--buildsystem=pybuild dh_strip -a -a -O--buildsystem=pybuild dh_makeshlibs -a -a -O--buildsystem=pybuild debian/rules override_dh_shlibdeps make[1]: Entering directory '/<>/python-cogent-2021.10.12a1+dfsg' dh_shlibdeps dh_numpy3 make[1]: Leaving directory '/<>/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 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing python3-cogent3 (in debian/python3-cogent3); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-cogent3/DEBIAN/control, package python3-cogent3, directory debian/python3-cogent3 pkgstripfiles: Truncating usr/share/doc/python3-cogent3/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-cogent3 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-cogent3' in '../python3-cogent3_2021.10.12a1+dfsg-1_s390x.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../python-cogent_2021.10.12a1+dfsg-1_s390x.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) -------------------------------------------------------------------------------- Build finished at 2021-11-04T17:39:09Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-cogent_2021.10.12a1+dfsg-1_s390x.changes: ------------------------------------------------ Format: 1.8 Date: Thu, 04 Nov 2021 09:29:04 +0100 Source: python-cogent Binary: python3-cogent3 Built-For-Profiles: noudeb Architecture: s390x Version: 2021.10.12a1+dfsg-1 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: python3-cogent3 - framework for genomic biology Changes: python-cogent (2021.10.12a1+dfsg-1) unstable; urgency=medium . * New upstream version * Upstream switched to filt build system Checksums-Sha1: f4b132dc8c6f149016c62bbce15eb29a302bbed7 11426 python-cogent_2021.10.12a1+dfsg-1_s390x.buildinfo a3b187d23843b60beb775da7b34a33a6a5fce3c6 1277272 python3-cogent3_2021.10.12a1+dfsg-1_s390x.deb Checksums-Sha256: c0380311c91554ffe7d7621f67d895fb3e24c209a4faabf5486f36b669e9281f 11426 python-cogent_2021.10.12a1+dfsg-1_s390x.buildinfo ede910e90941abaeed787f52dfe199db448b54aee064303175c0deb5f1d8bfb0 1277272 python3-cogent3_2021.10.12a1+dfsg-1_s390x.deb Files: bc72efcdef351534c615ce2c145c7fe8 11426 python optional python-cogent_2021.10.12a1+dfsg-1_s390x.buildinfo 936a53a6789b43a20a5f9dfd55769540 1277272 python optional python3-cogent3_2021.10.12a1+dfsg-1_s390x.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: python-cogent Binary: python3-cogent3 Architecture: s390x Version: 2021.10.12a1+dfsg-1 Checksums-Md5: 936a53a6789b43a20a5f9dfd55769540 1277272 python3-cogent3_2021.10.12a1+dfsg-1_s390x.deb Checksums-Sha1: a3b187d23843b60beb775da7b34a33a6a5fce3c6 1277272 python3-cogent3_2021.10.12a1+dfsg-1_s390x.deb Checksums-Sha256: ede910e90941abaeed787f52dfe199db448b54aee064303175c0deb5f1d8bfb0 1277272 python3-cogent3_2021.10.12a1+dfsg-1_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Thu, 04 Nov 2021 17:39:09 +0000 Build-Path: /<>/python-cogent-2021.10.12a1+dfsg Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20180224.1+nmu1), base-files (= 12ubuntu1), base-passwd (= 3.5.52), bash (= 5.1-3ubuntu2), binfmt-support (= 2.2.1-1), binutils (= 2.37-7ubuntu1), binutils-common (= 2.37-7ubuntu1), binutils-s390x-linux-gnu (= 2.37-7ubuntu1), black (= 21.4b2-3), bsdextrautils (= 2.37.2-4ubuntu1), bsdutils (= 1:2.37.2-4ubuntu1), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-4ubuntu4), ca-certificates (= 20211016), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-10ubuntu1), cython3 (= 0.29.24-0ubuntu3), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.3.4ubuntu3), debianutils (= 5.5-1), debugedit (= 1:5.0-0ubuntu2), dh-autoreconf (= 20), dh-python (= 5.20211022.1), dh-strip-nondeterminism (= 1.12.0-2), diffutils (= 1:3.8-0ubuntu1), docutils-common (= 0.17.1+dfsg-2), dpkg (= 1.20.9ubuntu2), dpkg-dev (= 1.20.9ubuntu2), dwz (= 0.14-1build1), file (= 1:5.39-3build1), findutils (= 4.8.0-1ubuntu2), flit (= 3.0.0-1), fonts-lyx (= 2.3.6-1), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-10ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-10ubuntu1), gcc-11-base (= 11.2.0-10ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), hostname (= 3.23ubuntu1), init-system-helpers (= 1.60build1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10ubuntu2), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-10ubuntu1), libatomic1 (= 11.2.0-10ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbinutils (= 2.37-7ubuntu1), libblas3 (= 3.9.0-3ubuntu3), libblkid1 (= 2.37.2-4ubuntu1), libbrotli1 (= 1.0.9-2build4), libbsd0 (= 0.11.3-1ubuntu3), libbz2-1.0 (= 1.0.8-4ubuntu4), libc-bin (= 2.34-0ubuntu3), libc-dev-bin (= 2.34-0ubuntu3), libc6 (= 2.34-0ubuntu3), libc6-dev (= 2.34-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build2), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-10ubuntu1), libcmark-gfm-extensions0 (= 0.29.0.gfm.0-6), libcmark-gfm0 (= 0.29.0.gfm.0-6), libcom-err2 (= 1.46.4-1ubuntu1), libcrypt-dev (= 1:4.4.18-4ubuntu2), libcrypt1 (= 1:4.4.18-4ubuntu2), libctf-nobfd0 (= 2.37-7ubuntu1), libctf0 (= 2.37-7ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.256ubuntu4), libdebhelper-perl (= 13.3.4ubuntu3), libdeflate0 (= 1.7-2ubuntu2), libdpkg-perl (= 1.20.9ubuntu2), libdw1 (= 0.185-2), libedit2 (= 3.1-20210910-1), libelf1 (= 0.185-2), libexpat1 (= 2.4.1-3), libexpat1-dev (= 2.4.1-3), libffi8 (= 3.4.2-1ubuntu5), libfile-stripnondeterminism-perl (= 1.12.0-2), libfreetype6 (= 2.11.0+dfsg-1), libfribidi0 (= 1.0.8-2ubuntu2), libgcc-11-dev (= 11.2.0-10ubuntu1), libgcc-s1 (= 11.2.0-10ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu2), libgdbm-compat4 (= 1.22-1), libgdbm6 (= 1.22-1), libgfortran5 (= 11.2.0-10ubuntu1), libglib2.0-0 (= 2.70.0-3), libgmp10 (= 2:6.2.1+dfsg-1ubuntu3), libgomp1 (= 11.2.0-10ubuntu1), libgpg-error0 (= 1.42-3), libgraphite2-3 (= 1.3.14-1build1), libgssapi-krb5-2 (= 1.18.3-7), libharfbuzz0b (= 2.7.4-1ubuntu2), libicu67 (= 67.1-7ubuntu1), libimagequant0 (= 2.12.2-1.1build1), libisl23 (= 0.24-2), libitm1 (= 11.2.0-10ubuntu1), libjbig0 (= 2.1-3.1build2), libjpeg-turbo8 (= 2.0.6-0ubuntu3), libjpeg8 (= 8c-2ubuntu8), libjs-jquery (= 3.5.1+dfsg+~3.5.5-8), libjs-jquery-hotkeys (= 0~20130707+git2d51e3a9+dfsg-2ubuntu1), libjs-jquery-isonscreen (= 1.2.0-1.1), libjs-jquery-metadata (= 12-3), libjs-jquery-tablesorter (= 1:2.31.3+dfsg1-2), libjs-jquery-throttle-debounce (= 1.1+dfsg.1-1.1), libjs-jquery-ui (= 1.12.1+dfsg-8), libjs-sphinxdoc (= 4.2.0-5), libjs-underscore (= 1.9.1~dfsg-4), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), liblapack3 (= 3.9.0-3ubuntu3), liblbfgsb0 (= 3.0+dfsg.3-9), liblcms2-2 (= 2.12~rc1-2build1), libllvm9 (= 1:9.0.1-16.1ubuntu1), liblz4-1 (= 1.9.3-2build1), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.39-3build1), libmagic1 (= 1:5.39-3build1), libmd0 (= 1.0.4-1), libmount1 (= 2.37.2-4ubuntu1), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2build1), libmpfr6 (= 4.1.0-3build2), libncursesw6 (= 6.2+20210905-1), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libopenjp2-7 (= 2.4.0-3), libpam-modules (= 1.4.0-10ubuntu1), libpam-modules-bin (= 1.4.0-10ubuntu1), libpam-runtime (= 1.4.0-10ubuntu1), libpam0g (= 1.4.0-10ubuntu1), libpcre2-8-0 (= 10.37-0ubuntu2), libpcre3 (= 2:8.39-13build4), libperl5.32 (= 5.32.1-3ubuntu3), libpfm4 (= 4.11.1+git32-gd0b85fb-1), libpipeline1 (= 1.5.3-1build1), libpng16-16 (= 1.6.37-3build4), libpython3-all-dev (= 3.9.4-1ubuntu2), libpython3-dev (= 3.9.4-1ubuntu2), libpython3-stdlib (= 3.9.4-1ubuntu2), libpython3.10 (= 3.10.0-3), libpython3.10-dev (= 3.10.0-3), libpython3.10-minimal (= 3.10.0-3), libpython3.10-stdlib (= 3.10.0-3), libpython3.9 (= 3.9.7-4), libpython3.9-dev (= 3.9.7-4), libpython3.9-minimal (= 3.9.7-4), libpython3.9-stdlib (= 3.9.7-4), libraqm0 (= 0.7.0-4), libreadline8 (= 8.1-2build1), libseccomp2 (= 2.5.1-1ubuntu2), libselinux1 (= 3.1-3build3), libsigsegv2 (= 2.13-1ubuntu2), libsmartcols1 (= 2.37.2-4ubuntu1), libsqlite3-0 (= 3.36.0-2), libssl1.1 (= 1.1.1l-1ubuntu1), libstdc++-11-dev (= 11.2.0-10ubuntu1), libstdc++6 (= 11.2.0-10ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 248.3-1ubuntu8), libtbb2 (= 2020.3-1), libtiff5 (= 4.3.0-2), libtinfo6 (= 6.2+20210905-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libubsan1 (= 11.2.0-10ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 248.3-1ubuntu8), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4ubuntu1), libwebp6 (= 0.6.1-2.1build1), libwebpdemux2 (= 0.6.1-2.1build1), libwebpmux3 (= 0.6.1-2.1build1), libxau6 (= 1:1.0.9-1build4), libxcb1 (= 1.14-3ubuntu2), libxdmcp6 (= 1:1.1.3-0ubuntu4), libxml2 (= 2.9.12+dfsg-5), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.13.0-19.19), llvm-9 (= 1:9.0.1-16.1ubuntu1), llvm-9-runtime (= 1:9.0.1-16.1ubuntu1), login (= 1:4.8.1-1ubuntu9), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 16), m4 (= 1.4.18-5ubuntu1), mailcap (= 3.70ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), media-types (= 4.0.0), mime-support (= 3.66), ncurses-base (= 6.2+20210905-1), ncurses-bin (= 6.2+20210905-1), openssl (= 1.1.1l-1ubuntu1), pandoc (= 2.9.2.1-1ubuntu4), pandoc-data (= 2.9.2.1-1ubuntu4), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), po-debconf (= 1.0.21+nmu1), python-babel-localedata (= 2.8.0+dfsg.1-7), python-matplotlib-data (= 3.3.4-2), python-pip-whl (= 20.3.4-4), python3 (= 3.9.4-1ubuntu2), python3-alabaster (= 0.7.12-1), python3-all (= 3.9.4-1ubuntu2), python3-all-dev (= 3.9.4-1ubuntu2), python3-appdirs (= 1.4.4-1), python3-attr (= 20.3.0-1), python3-babel (= 2.8.0+dfsg.1-7), python3-bleach (= 4.1.0-1), python3-certifi (= 2020.6.20-1), python3-chardet (= 4.0.0-1), python3-click (= 8.0.2-1), python3-colorama (= 0.4.4-1), python3-cov-core (= 1.15.0-3build1), python3-coverage (= 5.1+dfsg.1-2build2), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.1-6), python3-decorator (= 4.4.2-0ubuntu1), python3-defusedxml (= 0.7.1-1), python3-dev (= 3.9.4-1ubuntu2), python3-distlib (= 0.3.2+really+0.3.1-0.1), python3-distutils (= 3.9.7-1), python3-docutils (= 0.17.1+dfsg-2), python3-entrypoints (= 0.3-8), python3-filelock (= 3.3.2-1), python3-html5lib (= 1.1-3), python3-idna (= 2.10-1), python3-imagesize (= 1.2.0-2), python3-importlib-metadata (= 4.6.4-1), python3-iniconfig (= 1.1.1-1), python3-ipython-genutils (= 0.2.0-5), python3-isort (= 5.6.4-1), python3-jinja2 (= 3.0.1-2), python3-jsonschema (= 3.2.0-0ubuntu2), python3-jupyter-core (= 4.9.1-1), python3-kiwisolver (= 1.3.2-1), python3-lib2to3 (= 3.9.7-1), python3-llvmlite (= 0.35.0-3build1), python3-markupsafe (= 2.0.1-2), python3-matplotlib (= 3.3.4-2), python3-minimal (= 3.9.4-1ubuntu2), python3-mistune (= 0.8.4-5), python3-more-itertools (= 4.2.0-3), python3-mypy-extensions (= 0.4.3-2), python3-nbconvert (= 5.6.1-3), python3-nbformat (= 5.1.3-1), python3-nbsphinx (= 0.8.7+ds-1), python3-nose2 (= 0.9.2-1), python3-numba (= 0.52.0-4), python3-numpy (= 1:1.20.2-1ubuntu1), python3-numpydoc (= 1.1.0-3), python3-packaging (= 21.0-1), python3-pandas (= 1.1.5+dfsg-2ubuntu1), python3-pandas-lib (= 1.1.5+dfsg-2ubuntu1), python3-pandocfilters (= 1.4.3-1), python3-pathspec (= 0.9.0-1), python3-pil (= 8.3.2-1), python3-pip (= 20.3.4-4), python3-pkg-resources (= 58.2.0-1), python3-platformdirs (= 2.4.0-1), python3-pluggy (= 0.13.0-7.1), python3-py (= 1.10.0-1), python3-pygments (= 2.7.1+dfsg-2.1), python3-pyparsing (= 2.4.7-1), python3-pyrsistent (= 0.15.5-1build5), python3-pytest (= 6.2.5-1ubuntu1), python3-pytest-cov (= 3.0.0-1), python3-pytoml (= 0.1.21-1), python3-regex (= 0.1.20211008-1), python3-requests (= 2.25.1+dfsg-2), python3-roman (= 3.3-1), python3-scipy (= 1.7.1-1ubuntu1), python3-scitrack (= 2021.5.3-1), python3-setuptools (= 58.2.0-1), python3-six (= 1.16.0-2), python3-snowballstemmer (= 2.1.0-2), python3-sphinx (= 4.2.0-5), python3-sphinx-bootstrap-theme (= 0.8.0-1), python3-sphinx-gallery (= 0.10.0-1), python3-testpath (= 0.5.0+dfsg-1), python3-tinydb (= 3.15.2-2), python3-toml (= 0.10.2-1), python3-tqdm (= 4.57.0-2), python3-traitlets (= 5.1.1-1), python3-tz (= 2021.3-1), python3-urllib3 (= 1.26.5-1~exp1), python3-virtualenv (= 20.10.0+ds-1), python3-webencodings (= 0.5.1-4), python3-wheel (= 0.34.2-1), python3-zipp (= 1.0.0-3), python3.10 (= 3.10.0-3), python3.10-dev (= 3.10.0-3), python3.10-minimal (= 3.10.0-3), python3.9 (= 3.9.7-4), python3.9-dev (= 3.9.7-4), python3.9-minimal (= 3.9.7-4), readline-common (= 8.1-2build1), rpcsvc-proto (= 1.4.2-0ubuntu5), sed (= 4.7-1ubuntu2), sensible-utils (= 0.0.17), sgml-base (= 1.30), sphinx-common (= 4.2.0-5), sysvinit-utils (= 2.96-7ubuntu2), tar (= 1.34+dfsg-1build2), tox (= 3.21.4-1), ttf-bitstream-vera (= 1.10-8.1), tzdata (= 2021e-1ubuntu1), util-linux (= 2.37.2-4ubuntu1), xml-core (= 0.18+nmu1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1636014544" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python3-cogent3_2021.10.12a1+dfsg-1_s390x.deb --------------------------------------------- new Debian package, version 2.0. size 1277272 bytes: control archive=10085 bytes. 1670 bytes, 27 lines control 31563 bytes, 333 lines md5sums 267 bytes, 12 lines * postinst #!/bin/sh 416 bytes, 12 lines * prerm #!/bin/sh Package: python3-cogent3 Source: python-cogent Version: 2021.10.12a1+dfsg-1 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3767 Depends: black, flit, python3-chardet, python3-click, python3-ipykernel, python3-ipython, python3-ipywidgets, python3-isort, python3-jupyter-client, python3-jupyter-sphinx, python3-matplotlib, python3-nbconvert, python3-nbformat, python3-nbsphinx, python3-numba, python3-numpy (>= 1:1.20.0), python3-numpy-abi9, python3-numpydoc, python3-pandas, python3-pil, python3-plotly, python3-psutil, python3-pytest, python3-pytest-cov, python3-scitrack, python3-sphinx, python3-sphinx-autobuild, python3-sphinx-bootstrap-theme, python3-sphinx-gallery, python3-sphinxcontrib.bibtex, python3-tinydb, python3-tqdm, python3:any, tox Recommends: ncbi-blast+-legacy, dialign Suggests: python-cogent-doc Breaks: python-cogent Replaces: python-cogent Provides: python-cogent Section: python Priority: optional Homepage: https://github.com/cogent3/cogent3 Description: framework for genomic biology PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: * controlling third-party applications, * devising workflows; querying databases, * conducting novel probabilistic analyses of biological sequence evolution, and * generating publication quality graphics. 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python-cogent_2021.10.12a1+dfsg-1.dsc Machine Architecture: s390x Package: python-cogent Package-Time: 107 Source-Version: 2021.10.12a1+dfsg-1 Space: n/a Status: successful Version: 2021.10.12a1+dfsg-1 -------------------------------------------------------------------------------- Finished at 2021-11-04T17:39:09Z Build needed 00:01:47, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=s390x PACKAGEBUILD-22372250 Scanning for processes to kill in build PACKAGEBUILD-22372250