pysam 0.9.1

pysam

pysam - a python module for reading, manipulating and writing genomic data sets.

pysam is a lightweight 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 API for convenient access to the data within standard genomic file formats.

The current version wraps htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1.

See: http://www.htslib.org https://github.com/pysam-developers/pysam http://pysam.readthedocs.org/en/stable