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pysam: htslib interface for python
==================================
:Author: Andreas Heger, Kevin Jacobs and contributors
:Date: |today|
:Version: |version|
Pysam is a python module for reading, manipulating and writing
genomic data sets.
Pysam is a wrapper of the htslib_ C-API and provides facilities to
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well
as access to the command line functionality of the samtools_ and
bcftools_ packages. The module supports compression and random access
through indexing.
This module provides a low-level wrapper around the htslib_ C-API as
using cython and a high-level, pythonic API for convenient access to
the data within genomic file formats.
The current version wraps *htslib-1.7*, *samtools-1.7* and
*bcftools-1.6*.
To install the latest release, type::
pip install pysam
See the :ref:`Installation notes <installation>` for details.
Contents
--------
.. toctree::
:maxdepth: 2
api.rst
usage.rst
installation.rst
faq.rst
developer.rst
release.rst
benchmarking.rst
glossary.rst
Indices and tables
------------------
Contents:
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
References
----------
.. [Li2009] The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup.
Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8.
`PMID: 19505943 <http://www.ncbi.nlm.nih.gov/pubmed/19505943?dopt=Abstract>`_
.. seealso::
Information about htslib
http://www.htslib.org
The samtools homepage
http://samtools.sourceforge.net
The cython C-extensions for python
http://cython.org/
The python language
http://www.python.org
|
