| 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-1.3, samtools-1.3 and bcftools-1.3.
To install the latest release, type:
pip install pysam
See the :ref:`Installation notes <installation>` for details.
.. toctree:: :maxdepth: 2 api.rst usage.rst installation.rst faq.rst developer.rst release.rst glossary.rst
Contents:
| [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 |
.. 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