ngslib 1.1.20

Python Modules for Next-Generation Sequencing Data Analysis.

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.