pytabix

This module allows fast random access to sorted 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.

Alternatives:

• Instead of using this module, you can install tabix yourself and easily call it from Python as shown at the bottom of this page.
• pysam - A python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
• hts-python - A pythonic wrapper for htslib C-API using python cffi.

Synopsis

Open a local or remote file that has already been sorted, compressed, and indexed:

import tabix

url = "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/"
url += "ALL.2of4intersection.20100804.genotypes.vcf.gz"

tb = tabix.open(url)

records = tb.query("1", 1000000, 1250000)
records = tb.queryi(0, 1000000, 1250000)
records = tb.querys("1:1000000-1250000")

for record in records:
    print record[:3]

['1', '1000760', 'rs75316104']
['1', '1000760', 'rs75316104']
['1', '1000894', 'rs114006445']
['1', '1000910', 'rs79750022']
['1', '1001177', 'rs4970401']
['1', '1001256', 'rs78650406']

Install

pip install --user pytabix

or

wget https://pypi.python.org/packages/source/p/pytabix/pytabix-0.0.2.tar.gz
tar xf pytabix-0.0.2.tar.gz
cd pytabix-0.0.2
python setup.py install --user

Contributing

Please submit an issue to report bugs or ask questions.

Please contribute bug fixes or new features with a pull request to this repository.

How to prepare a file for tabix

1. Sort the file by chromosome, start, and end.
2. Compress the file with bgzip.
3. Index the compressed file with tabix.

$ head -n5 example.bed | column -t
chr19  53611131   53636172   ZNF415
chr10  72149121   72150375   CEP57L1P1
chr4   185009858  185139113  ENPP6
chrX   132669772  133119672  GPC3
chr6   134924279  134925376  FAM8A6P

1. Sort it by chromosome, start, and end.
2. Then, use bgzip to deflate the file into compressed blocks:

$ sort -k1V -k2n -k3n example.bed | bgzip > example.bed.gz

3. Index the compressed file with tabix:

$ tabix -s 1 -b 2 -e 3 example.bed.gz

$ ls
example.bed  example.bed.gz  example.bed.gz.tbi

Alternative: Use subprocess

from subprocess import Popen, PIPE

def bgzip(filename):
    """Call bgzip to compress a file."""
    Popen(['bgzip', '-f', filename])

def tabix_index(filename,
        preset="gff", chrom=1, start=4, end=5, skip=0, comment="#"):
    """Call tabix to create an index for a bgzip-compressed file."""
    Popen(['tabix', '-p', preset, '-s', chrom, '-b', start, '-e', end,
        '-S', skip, '-c', comment])

def tabix_query(filename, chrom, start, end):
    """Call tabix and generate an array of strings for each line it returns."""
    query = '{}:{}-{}'.format(chrom, start, end)
    process = Popen(['tabix', '-f', filename, query], stdout=PIPE)
    for line in process.stdout:
        yield line.strip().split()