pysam: htslib interface for python

Author:Andreas Heger, Kevin Jacobs and contributors Date:Jun 18, 2017 Version:0.11.2.2

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 Installation notes for details.

Contents

• pysam - An interface for reading and writing SAM files
  • Introduction
  • API
• Working with BAM/CRAM/SAM-formatted files
  • Opening a file
  • Fetching reads mapped to a region
  • Using the pileup-engine
  • Creating BAM/CRAM/SAM files from scratch
  • Using streams
• Using samtools commands within python
• Working with tabix-indexed files
• Working with VCF/BCF formatted files
• Extending pysam
• Installing pysam
  • Builtin
  • External
  • cython
• FAQ
  • How should I cite pysam
  • Is pysam thread-safe?
  • pysam coordinates are wrong
  • Calling pysam.fetch() confuses existing iterators
  • AlignmentFile.fetch does not show unmapped reads
  • I can’t call AlignmentFile.fetch on a file without index
  • BAM files with a large number of reference sequences are slow
  • Weirdness with spliced reads in samfile.pileup(chr,start,end) given spliced alignments from an RNA-seq bam file
  • I can’t edit quality scores in place
  • Why is there no SNPCaller class anymore?
  • I get an error ‘PileupProxy accessed after iterator finished’
  • Pysam won’t compile
• Developer’s guide
  • Code organization
  • Importing new versions of htslib and samtools
  • Unit testing
  • Contributors
• Release notes
  • Release 0.11.2.2
  • Release 0.11.2.1
  • Release 0.11.2
  • Release 0.11.1
  • Release 0.11.0
  • Release 0.10.0
  • Release 0.9.1
  • Release 0.9.0
  • Release 0.8.4
  • Release 0.8.3
  • Release 0.8.2.1
  • Release 0.8.2
  • Release 0.8.1
  • Release 0.8.0
  • Release 0.7.8
  • Release 0.7.7
  • Release 0.7.6
  • Release 0.7.5
  • Release 0.7.4
  • Release 0.7.3
  • Release 0.7.2
  • Release 0.7.1
  • Release 0.7
  • Release 0.6
  • Release 0.5
  • Release 0.4
  • Release 0.3
• Glossary

Indices and tables

Contents:

• Index
• Module Index
• Search Page

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

See also

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