ngslib

ngslib current release: ngslib 1.1.19

Wiki page moved to GitHub.

Requirement

• numpy scientific computation
• pysam (>0.8.2) SAM/BAM file manipulation
• argparse (required if Python2.6 is used)

Tested on

• Python 2.6.* (64-bit)
• Python 2.7.* (64-bit)
• CentOS 6.4
• Fedora 17
• RedHat 5.5
• Ubuntu 12.04 (python-dev and libpng-dev are required)

Installation

From PyPI:

>>> pip install ngslib

or

>>> easy_install ngslib

From source:

>>> easy_install --editable  --build-directory . ngslib
>>> cd ngslib
>>> python setup.py install

Major modules

• IO: Read various biological data
• DB: Build DB for genomic data for fast query.
• Pipeline: Pipelines built using wrappers of commonly used tools.
• Bed: Genomic coordinates data format.
• BedList: A list of Bed instances.
• TwoBitFile: python module for retrieve fasta sequence from 2bit file.
• BigWigFile: python module for retrieve Wiggle region from BigWig file.
• mFile: uniform interface for input types including regular file, sys.stdin/stdout and StringFile.

Usage

>>> import ngslib
>>> for tbed in ngslib.IO.BioReader('test.bed','bed'):
        print tbed

>>> bwf = ngslib.DB('test.bw','bigwig')
>>> for wig in bwf.fetch('chr1',1000,2000):
        print wig
>>> depth = bwf.pileup('chr1',3000,4000)
>>> bwf.close()

License

This program is released under GPLv3 license, see LICENSE for more detail.