wip/py-pysam 0.21.0 NetBSD

Python module for reading, manipulating and writing genomic data sets

System: NetBSD
Repository: pkgsrc-wip
Maintainer: [email protected]
License: mit
Categories: wip, biology

Description

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.

Install

From pkgsrc-wip (no binary package):

cd /usr/pkgsrc/wip/py-pysam && make install clean

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["wip/py-pysam"]
  u0["wip/nanoget"] --> me
  u1["wip/nanostat"] --> me
  u2["wip/py-htseq"] --> me
  me --> d0["biology/htslib"]
  me --> d1["devel/zlib"]
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

Run dependencies 2

Required by 3