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_.

.. _pysam: https://github.com/pysam-developers/pysam .. _hts-python: https://github.com/brentp/hts-python .. _htslib: https://github.com/samtools/htslib .. _cffi: https://cffi.readthedocs.org

Synopsis

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

.. code:: python

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]

.. code:: python

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

Install

.. code:: bash

pip install --user pytabix

or

.. code:: bash

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.

__ https://github.com/slowkow/pytabix/issues

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

__ https://help.github.com/articles/using-pull-requests/

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_.

.. code:: bash

$ 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:

.. code:: bash

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

3. Index the compressed file with tabix_:

.. code:: bash

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

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

Alternative: Use subprocess

.. code:: python

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()

.. _bgzip: http://samtools.sourceforge.net/tabix.shtml .. _tabix: http://samtools.sourceforge.net/tabix.shtml .. _klib: https://github.com/jmarshall/klib .. _here: http://sourceforge.net/projects/samtools/files/tabix/ .. _Sort: https://www.gnu.org/software/coreutils/manual/html_node/Details-about-version-sort.html#Details-about-version-sort