Overview
--------
.. image:: https://badge.fury.io/py/pybedtools.svg?style=flat
:target: https://badge.fury.io/py/pybedtools
.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
:target: https://bioconda.github.io
The `BEDTools suite of programs <http://bedtools.readthedocs.org/>`_ 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
https://daler.github.io/pybedtools/.
The GitHub repo is at https://github.com/daler/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 <http://daler.github.io/pybedtools/sh-comparison.html>`_ in the docs
for more details on this comparison, or keep reading the full documentation at
http://daler.github.io/pybedtools.
Raw data
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"description": "\nOverview\n--------\n\n.. image:: https://badge.fury.io/py/pybedtools.svg?style=flat\n :target: https://badge.fury.io/py/pybedtools\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg\n :target: https://bioconda.github.io\n\nThe `BEDTools suite of programs <http://bedtools.readthedocs.org/>`_ is widely\nused for genomic interval manipulation or \"genome algebra\". `pybedtools` wraps\nand extends BEDTools and offers feature-level manipulations from within\nPython.\n\nSee full online documentation, including installation instructions, at\nhttps://daler.github.io/pybedtools/.\n\nThe GitHub repo is at https://github.com/daler/pybedtools.\n\nWhy `pybedtools`?\n-----------------\n\nHere is an example to get the names of genes that are <5 kb away from\nintergenic SNPs:\n\n.. code-block:: python\n\n from pybedtools import BedTool\n\n snps = BedTool('snps.bed.gz') # [1]\n genes = BedTool('hg19.gff') # [1]\n\n intergenic_snps = snps.subtract(genes) # [2]\n nearby = genes.closest(intergenic_snps, d=True, stream=True) # [2, 3]\n\n for gene in nearby: # [4]\n if int(gene[-1]) < 5000: # [4]\n print gene.name # [4]\n\nUseful features shown here include:\n\n* `[1]` support for all BEDTools-supported formats (here gzipped BED and GFF)\n* `[2]` wrapping of all BEDTools programs and arguments (here, `subtract` and `closest` and passing\n the `-d` flag to `closest`);\n* `[3]` streaming results (like Unix pipes, here specified by `stream=True`)\n* `[4]` iterating over results while accessing feature data by index or by attribute\n access (here `[-1]` and `.name`).\n\nIn contrast, here is the same analysis using shell scripting. Note that this\nrequires knowledge in Perl, bash, and awk. The run time is identical to the\n`pybedtools` version above:\n\n.. code-block:: bash\n\n snps=snps.bed.gz\n genes=hg19.gff\n intergenic_snps=/tmp/intergenic_snps\n\n snp_fields=`zcat $snps | awk '(NR == 2){print NF; exit;}'`\n gene_fields=9\n distance_field=$(($gene_fields + $snp_fields + 1))\n\n intersectBed -a $snps -b $genes -v > $intergenic_snps\n\n closestBed -a $genes -b $intergenic_snps -d \\\n | awk '($'$distance_field' < 5000){print $9;}' \\\n | perl -ne 'm/[ID|Name|gene_id]=(.*?);/; print \"$1\\n\"'\n\n rm $intergenic_snps\n\nSee the `Shell script comparison <http://daler.github.io/pybedtools/sh-comparison.html>`_ in the docs\nfor more details on this comparison, or keep reading the full documentation at\nhttp://daler.github.io/pybedtools.\n",
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