Python Modules for Next-Generation Sequencing Data Analysis.
Project description
ngslib current release: ngslib 1.1.19
Wiki page moved to GitHub.
Requirement
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.
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