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