https://github.com/arq5x/cyvcf

A fast Python library for VCF files leveraging Cython for speed.
https://github.com/arq5x/cyvcf

Last synced: about 2 months ago
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A fast Python library for VCF files leveraging Cython for speed.

• Host: GitHub
• URL: https://github.com/arq5x/cyvcf
• Owner: arq5x
• License: mit
• Created: 2012-04-12T18:51:06.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2018-03-27T09:31:09.000Z (over 6 years ago)
• Last Synced: 2024-05-09T09:31:24.972Z (4 months ago)
• Language: Python
• Homepage:
• Size: 1.54 MB
• Stars: 52
• Watchers: 6
• Forks: 13
• Open Issues: 12
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

• Awesome-Bioinformatics - cyvcf - A port of [pyVCF](https://github.com/jamescasbon/PyVCF) using Cython for speed. (Next Generation Sequencing / Python Modules)

README

        
CyVCF

======

A Cython port of the PyVCF library maintained by @jamescasbon.

The goal of this project is to provide a very fast Python library for parsing and manipulating large VCF files.

Cython has been used to optimize speed.  This version is approximately 4 times faster than PyVCF,

and the parsing speed is essentially identical to that of C/C++ libraries provided by PLINKSEQ and VCFLIB.

The functionality and interface are currently the same as documented here: http://pyvcf.rtfd.org/

Installation

============

    python setup.py build

    python setup.py install

Testing

=======

    python setup.py test

Basic usage

===========

    >>> import cyvcf

    >>> vcf_reader = cyvcf.Reader(open('test/example-4.0.vcf', 'rb'))

    >>> for record in vcf_reader:

    ...     print record

    20	14370	G	A	29.0	.	H2=True;NS=3;DB=True;DP=14;AF=0.5	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.

    20	17330	T	A	3.0	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.

    20	1110696	A	G,T	67.0	.	AA=T;NS=2;DB=True;DP=10;AF=0.333,0.667	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.

    20	1230237	T	.	47.0	.	AA=T;NS=3;DP=13	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:.

    20	1234567	GTCT	G,GTACT	50.0	.	AA=G;NS=3;DP=9	GT:GQ:DP	./.	0/2:17:2	1/1:40:3