This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
Project Description

Python bindings for ngslib library

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.

Release History

Release History

1.1.19

This version

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1.1.18

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1.1.17

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1.1.15

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1.1.14

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1.1.13

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1.1.12

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1.1.11

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1.1.10

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1.1.9

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1.1.8

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1.1.7

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1.1.6

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1.1.5

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1.1.4

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1.1.3

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1.1.2

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1.1.1

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1.1.0

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
ngslib-1.1.19.tar.gz (1.1 MB) Copy SHA256 Checksum SHA256 Source Sep 16, 2016

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