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Python Modules for Next-Generation Sequencing Data Analysis.

Project description

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.

Project details


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