pytabix 0.0.2

Python interface for tabix

April 16, 2014

This module allows fast random access to files compressed with bgzip and indexed by tabix. It includes a C extension with code from klib. The bgzip and tabix programs are available here.

Installation

pip install --user pytabix

Synopsis

Genomics data is often in a table where each row corresponds to a genomic region (start, end) or a position:

chrom  pos      snp
1      1000760  rs75316104
1      1000894  rs114006445
1      1000910  rs79750022
1      1001177  rs4970401
1      1001256  rs78650406

With tabix, you can quickly retrieve all rows in a genomic region by specifying a query with a sequence name, start, and end:

import tabix

# Open a remote or local file.
url = "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/"
url += "ALL.2of4intersection.20100804.genotypes.vcf.gz"

tb = tabix.open(url)

# These queries are identical. A query returns an iterator over the results.
records = tb.query("1", 1000000, 1250000)

records = tb.queryi(0, 1000000, 1250000)

records = tb.querys("1:1000000-1250000")

# Each record is a list of strings.
for record in records:
    print record[:5]
    break

['1', '1000071', '.', 'C', 'T']