https://github.com/pysam-developers/pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://github.com/pysam-developers/pysam

Last synced: about 2 months ago
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Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

• Host: GitHub
• URL: https://github.com/pysam-developers/pysam
• Owner: pysam-developers
• License: mit
• Created: 2014-02-05T20:38:10.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2024-04-20T10:17:19.000Z (5 months ago)
• Last Synced: 2024-04-20T12:44:23.629Z (5 months ago)
• Language: Cython
• Homepage: https://pysam.readthedocs.io/en/latest/
• Size: 19.1 MB
• Stars: 750
• Watchers: 48
• Forks: 269
• Open Issues: 272
• Metadata Files:
  • Readme: README.rst
  • License: COPYING
  • Authors: AUTHORS

Awesome Lists containing this project

• Awesome-Bioinformatics - pysam - Python wrapper for [samtools](https://github.com/samtools/samtools). [ [web](https://pysam.readthedocs.io/en/latest/api.html) ] (Next Generation Sequencing / Python Modules)

README

        
=====

Pysam

=====

|build-status| |docs|

Pysam is a python module for reading and manipulating files in the

SAM/BAM format. The SAM/BAM format is a way to store efficiently large

numbers of alignments (`Li 2009`_), such as those routinely created by

next-generation sequencing methods.

Pysam is a lightweight wrapper of the samtools_ C-API. Pysam also

includes an interface for tabix_.

If you are using the conda packaging manager (e.g. miniconda or anaconda),

you can install pysam from the `bioconda channel `_::

   conda config --add channels defaults

   conda config --add channels conda-forge

   conda config --add channels bioconda

   conda install pysam

Installation through bioconda is the recommended way to install pysam

as it resolves non-python dependencies and uses pre-configured

compilation options. Especially for OS X this will potentially save a

lot of trouble.

The current version of pysam wraps 3rd-party code from htslib-1.18, samtools-1.18, and bcftools-1.18.

Pysam is available through `pypi

`_. To install, type::

   pip install pysam

Pysam documentation is available

`here `_

Questions and comments are very welcome and should be sent to the

`pysam user group `_

.. _samtools: http://samtools.sourceforge.net/

.. _tabix: http://samtools.sourceforge.net/tabix.shtml

.. _Li 2009: http://www.ncbi.nlm.nih.gov/pubmed/19505943

.. |build-status| image:: https://github.com/pysam-developers/pysam/actions/workflows/ci.yaml/badge.svg

    :alt: build status

    :scale: 100%

    :target: https://github.com/pysam-developers/pysam/actions/workflows/ci.yaml

.. |docs| image:: https://readthedocs.org/projects/pysam/badge/?version=latest

    :alt: Documentation Status

    :scale: 100%

    :target: https://pysam.readthedocs.org/en/latest/?badge=latest