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)

Property Value
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

Package Version Architecture Repository
python-biom-format_2.1.5+dfsg-1_i386.deb 2.1.5+dfsg i386 Ubuntu Universe
python-biom-format - - -

Requires

Name Value
libc6 >= 2.4
pyqi -
python << 2.8
python >= 2.7~
python-click -
python-future -
python-numpy >= 1:1.10.0~b1
python-numpy-abi9 -
python-scipy -
python:any >= 2.7.5-5~

Download

Type URL
Binary Package python-biom-format_2.1.5+dfsg-1_amd64.deb
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

Path
/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

See Also

Package Description
python-biopython-doc_1.66+dfsg-1build1_all.deb Documentation for the Biopython library
python-biopython-sql_1.66+dfsg-1build1_all.deb Biopython support for the BioSQL database schema (Python 2)
python-biopython_1.66+dfsg-1build1_amd64.deb Python library for bioinformatics (implemented in Python 2)
python-biosig_1.3.0-2.1build1_amd64.deb Python bindings for BioSig library
python-biplist_0.7-1_all.deb Python library for reading/writing Mac OS X binary plists
python-bitarray_0.8.1-1build2_amd64.deb Python module for efficient boolean array handling
python-bitbucket_0.1-1_all.deb Python bindings for the bitbucket.org REST API
python-bitstring-doc_3.1.4-1_all.deb Python module for manipulation of binary data (documentation)
python-bitstring_3.1.4-1_all.deb Python module for manipulation of binary data (Python 2)
python-bittorrent_3.4.2-12_all.deb Scatter-gather network file transfer
python-bjsonrpc_0.2.0-2_all.deb asynchronous bidirectional JSON-RPC protocol over TCP/IP
python-bleach-doc_1.4.2-1_all.deb whitelist-based HTML-sanitizing library (common documentation)
python-bleach_1.4.2-1_all.deb whitelist-based HTML-sanitizing library (Python 2)
python-blessings_1.6-2build1_all.deb simple but powerful module to manage terminal color and styling (Python 2)
python-blist_1.3.6-4build2_amd64.deb List-like type for Python with better asymptotic performance
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