ngslib current release: ngslib 1.1.19
Wiki page moved to GitHub.
- numpy scientific computation
- pysam (>0.8.2) SAM/BAM file manipulation
- argparse (required if Python2.6 is used)
Python 2.6.*
(64-bit)Python 2.7.*
(64-bit)CentOS 6.4
Fedora 17
RedHat 5.5
Ubuntu 12.04
(python-dev
andlibpng-dev
are required)
From PyPI:
>>> pip install ngslib
or
>>> easy_install ngslib
From source:
>>> easy_install --editable --build-directory . ngslib
>>> cd ngslib
>>> python setup.py install
- 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.
>>> 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()
This program is released under GPLv3
license, see LICENSE
for more detail.