pybedtools

by daler

daler / pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

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Overview

.. image:: https://travis-ci.org/daler/pybedtools.png?branch=master :target: https://travis-ci.org/daler/pybedtools

.. image:: https://badge.fury.io/py/pybedtools.svg?style=flat :target: http://badge.fury.io/py/pybedtools

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg :target: http://bioconda.github.io

The

BEDTools suite of programs 
_ is widely used for genomic interval manipulation or "genome algebra".
pybedtools
wraps and extends BEDTools and offers feature-level manipulations from within Python.

See full online documentation, including installation instructions, at http://daler.github.io/pybedtools/.

Why
pybedtools
?

Here is an example to get the names of genes that are <5 kb away from intergenic SNPs:

.. code-block:: python

from pybedtools import BedTool

snps = BedTool('snps.bed.gz') # [1] genes = BedTool('hg19.gff') # [1]

intergenic_snps = snps.subtract(genes) # [2] nearby = genes.closest(intergenic_snps, d=True, stream=True) # [2, 3]

for gene in nearby: # [4] if int(gene[-1]) < 5000: # [4] print gene.name # [4]

Useful features shown here include:

  • [1]
    support for all BEDTools-supported formats (here gzipped BED and GFF)
  • [2]
    wrapping of all BEDTools programs and arguments (here,
    subtract
    and
    closest
    and passing the
    -d
    flag to
    closest
    );
  • [3]
    streaming results (like Unix pipes, here specified by
    stream=True
    )
  • [4]
    iterating over results while accessing feature data by index or by attribute access (here
    [-1]
    and
    .name
    ).

In contrast, here is the same analysis using shell scripting. Note that this requires knowledge in Perl, bash, and awk. The run time is identical to the

pybedtools
version above:

.. code-block:: bash

snps=snps.bed.gz
genes=hg19.gff
intergenic_snps=/tmp/intergenic_snps

snp_fields=zcat $snps | awk '(NR == 2){print NF; exit;}' gene_fields=9 distance_field=$(($gene_fields + $snp_fields + 1))

intersectBed -a $snps -b $genes -v > $intergenic_snps

closestBed -a $genes -b $intergenic_snps -d
| awk '($'$distance_field' < 5000){print $9;}'
| perl -ne 'm/[ID|Name|gene_id]=(.*?);/; print "$1\n"'

rm $intergenic_snps

See the

Shell script comparison 
_ in the docs for more details on this comparison, or keep reading the full documentation at http://daler.github.io/pybedtools.

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