Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

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
JSON representation

A fast Python library for VCF files leveraging Cython for speed.

Awesome Lists containing this project

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