A fast Python library for VCF files using Cython for speed.
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/
python setup.py build python setup.py install
python setup.py test
>>> 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