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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.
- 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: 2024-10-14T15:14:36.203Z (2 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 installTesting
=======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