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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 <https://bioconda.github.io/>_::
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 <https://pypi.python.org/pypi/pysam>_. To install, type::
pip install pysam
Pysam documentation is available
here <http://pysam.readthedocs.org/en/latest/>_
Questions and comments are very welcome and should be sent to the
pysam user group <http://groups.google.com/group/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
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