python-biom-format_2.1.5+dfsg-1_amd64.deb


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Description

python-biom-format - Biological Observation Matrix (BIOM) format (Python 2)

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe amd64
Package name: python-biom-format
Package version: 2.1.5+dfsg
Package release: 1
Package architecture: amd64
Package type: deb
Installed size: 1.55 KB
Download size: 160.51 KB
Official Mirror: archive.ubuntu.com
The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project. The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. This package provides the BIOM format library for the Python 2 interpreter.

Alternatives

    Download

    Source package: python-biom-format

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install python-biom-format deb package:
      # sudo apt-get install python-biom-format

    Files

    • /usr/lib/python2.7/dist-packages/biom/__init__.py
    • /usr/lib/python2.7/dist-packages/biom/_filter.c
    • /usr/lib/python2.7/dist-packages/biom/_filter.pyx
    • /usr/lib/python2.7/dist-packages/biom/_filter.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/biom/_subsample.c
    • /usr/lib/python2.7/dist-packages/biom/_subsample.pyx
    • /usr/lib/python2.7/dist-packages/biom/_subsample.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/biom/_transform.c
    • /usr/lib/python2.7/dist-packages/biom/_transform.pyx
    • /usr/lib/python2.7/dist-packages/biom/_transform.x86_64-linux-gnu.so
    • /usr/lib/python2.7/dist-packages/biom/err.py
    • /usr/lib/python2.7/dist-packages/biom/exception.py
    • /usr/lib/python2.7/dist-packages/biom/parse.py
    • /usr/lib/python2.7/dist-packages/biom/table.py
    • /usr/lib/python2.7/dist-packages/biom/util.py
    • /usr/lib/python2.7/dist-packages/biom/cli/__init__.py
    • /usr/lib/python2.7/dist-packages/biom/cli/installation_informer.py
    • /usr/lib/python2.7/dist-packages/biom/cli/metadata_adder.py
    • /usr/lib/python2.7/dist-packages/biom/cli/table_converter.py
    • /usr/lib/python2.7/dist-packages/biom/cli/table_head.py
    • /usr/lib/python2.7/dist-packages/biom/cli/table_normalizer.py
    • /usr/lib/python2.7/dist-packages/biom/cli/table_subsetter.py
    • /usr/lib/python2.7/dist-packages/biom/cli/table_summarizer.py
    • /usr/lib/python2.7/dist-packages/biom/cli/table_validator.py
    • /usr/lib/python2.7/dist-packages/biom/cli/uc_processor.py
    • /usr/lib/python2.7/dist-packages/biom/cli/util.py
    • /usr/lib/python2.7/dist-packages/biom_format-2.1.5.egg-info/PKG-INFO
    • /usr/lib/python2.7/dist-packages/biom_format-2.1.5.egg-info/dependency_links.txt
    • /usr/lib/python2.7/dist-packages/biom_format-2.1.5.egg-info/entry_points.txt
    • /usr/lib/python2.7/dist-packages/biom_format-2.1.5.egg-info/requires.txt
    • /usr/lib/python2.7/dist-packages/biom_format-2.1.5.egg-info/top_level.txt
    • /usr/lib/python2.7/dist-packages/examples/min_sparse_otu_table.biom
    • /usr/lib/python2.7/dist-packages/examples/min_sparse_otu_table_hdf5.biom
    • /usr/lib/python2.7/dist-packages/examples/obs_md.txt
    • /usr/lib/python2.7/dist-packages/examples/rich_sparse_otu_table.biom
    • /usr/lib/python2.7/dist-packages/examples/rich_sparse_otu_table_hdf5.biom
    • /usr/lib/python2.7/dist-packages/examples/sam_md.txt
    • /usr/share/doc/python-biom-format/changelog.Debian.gz
    • /usr/share/doc/python-biom-format/copyright

    Changelog

    2016-03-08 - Andreas Tille <tille@debian.org> python-biom-format (2.1.5+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * Removed pyqi as well as generation of bash_completion * Build-Depends: python-click [ Ghislain Antony Vaillant ] * Properly run the upstream testsuite during the package build process * Add packaging testsuite * Provide documentation in separate arch-independent package * d/rules: add call to dh_numpy * let dh_python fill the binary package dependencies * Provide command-line tools in separate package * Provide the Python 3 package

    2015-11-10 - Andreas Tille <tille@debian.org> python-biom-format (2.1.4+dfsg-2) unstable; urgency=medium * Fix test target Closes: #804441 * Fix clean target enabling building twice in a row

    2015-10-27 - Andreas Tille <tille@debian.org> python-biom-format (2.1.4+dfsg-1) unstable; urgency=medium * New upstream version Closes: #802867 * Moved from SVN to Git * cme fix dpkg-control * Fix watch file

    2014-08-12 - Andreas Tille <tille@debian.org> python-biom-format (2.1+dfsg-1) unstable; urgency=medium * New upstream version

    2014-05-20 - Andreas Tille <tille@debian.org> python-biom-format (2.0.0+dfsg-1) unstable; urgency=medium * New upstream version (adpated Build-Depends and patches) * switch to dh-python using buildsystem=pybuild * New (versioned) Build-Depends * Add ${shlibs:Depends} since package is now arch any

    2014-03-27 - Andreas Tille <tille@debian.org> python-biom-format (1.3.1+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version (updated patches). New version also does not use Cython Closes: #742691 * Package is now Architecture: all * Incorporate changes by BioLinux * debian/patches/no-web-adds.patch: Save user privacy by preventing inclusion of web adds * Do not install scripts printing "This script no longer exists. ..." any more * Use manpage created by sphinx

    2014-02-28 - Tim Booth <tbooth@ceh.ac.uk> python-biom-format (1.2.0-1biolinux1) precise; urgency=low * Add runtime dep on PyQi * Patch /usr/bin/biom script to force /usr/lib/python2.7/dist-packages to the top of the PYTHONPATH * Allow building with cython 0.15.1 on Ubuntu as it builds and passes all the tests * Drop deal_with_none_array_metadata for now as it fails the self tests But it's still not right! * Rename add_metadata to something less generic. It will die in the next release anyway.

    2013-11-11 - Andreas Tille <tille@debian.org> python-biom-format (1.2.0-1) unstable; urgency=low * New upstream version * debian/control: - (Build-)Depends: pyqi - Build-Depends: python-nose to enable auto_test * debian/biom.1: Add simple manpage * debian/rules: - activate test using python-nose - deactivate get-orig-source script and use plain uscan since upstream tarball is clean now

    2013-09-25 - Tim Booth <tbooth@ceh.ac.uk> python-biom-format (1.2.0-0biolinux2) precise; urgency=low * New upstream. * No need for the old cythonize tinkering in rules * Add examples to /usr/share/doc * Also add HTML API docs (single html build) * Build manpages from Sphinx * Add bash completion * Investigate and patch issue converting BIOM to table with taxonomy not set to an array

    2013-08-15 - Andreas Tille <tille@debian.org> python-biom-format (1.1.2-1) unstable; urgency=low * debian/watch: - Enable '+dfsg' suffix in Debian versions - Fix download location - anonscm in Vcs fields * debian/control: - cme fix dpkg-control * Remove workaround cython problem which was needed when 1.0.0 was released because cython at this time was suffering from #682652 * debian/rules: - use help2man to create manpages

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