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 pytabixor
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 --userContributing
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
- Sort the file by chromosome, start, and end.
- Compress the file with bgzip.
- 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$ sort -k1V -k2n -k3n example.bed | bgzip > example.bed.gz- 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.tbiAlternative: 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()
