jpayne@68: Metadata-Version: 2.1
jpayne@68: Name: pybedtools
jpayne@68: Version: 0.11.0
jpayne@68: Summary: Wrapper around BEDTools for bioinformatics work
jpayne@68: Home-page: https://github.com/daler/pybedtools
jpayne@68: Download-URL: 
jpayne@68: Maintainer: Ryan Dale
jpayne@68: Maintainer-email: ryan.dale@nih.gov
jpayne@68: License: MIT
jpayne@68: Classifier: Development Status :: 5 - Production/Stable
jpayne@68: Classifier: Intended Audience :: Science/Research
jpayne@68: Classifier: License :: OSI Approved :: MIT License
jpayne@68: Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
jpayne@68: Classifier: Programming Language :: Python
jpayne@68: Classifier: Programming Language :: Python :: 3
jpayne@68: Classifier: Programming Language :: Python :: 3.6
jpayne@68: Classifier: Programming Language :: Python :: 3.7
jpayne@68: Classifier: Programming Language :: Python :: 3.8
jpayne@68: Classifier: Topic :: Software Development :: Libraries :: Python Modules
jpayne@68: License-File: LICENSE.txt
jpayne@68: Requires-Dist: pysam
jpayne@68: Requires-Dist: numpy
jpayne@68: 
jpayne@68: 
jpayne@68: Overview
jpayne@68: --------
jpayne@68: 
jpayne@68: .. image:: https://badge.fury.io/py/pybedtools.svg?style=flat
jpayne@68:     :target: https://badge.fury.io/py/pybedtools
jpayne@68: 
jpayne@68: .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
jpayne@68:     :target: https://bioconda.github.io
jpayne@68: 
jpayne@68: The `BEDTools suite of programs <http://bedtools.readthedocs.org/>`_ is widely
jpayne@68: used for genomic interval manipulation or "genome algebra".  `pybedtools` wraps
jpayne@68: and extends BEDTools and offers feature-level manipulations from within
jpayne@68: Python.
jpayne@68: 
jpayne@68: See full online documentation, including installation instructions, at
jpayne@68: https://daler.github.io/pybedtools/.
jpayne@68: 
jpayne@68: The GitHub repo is at https://github.com/daler/pybedtools.
jpayne@68: 
jpayne@68: Why `pybedtools`?
jpayne@68: -----------------
jpayne@68: 
jpayne@68: Here is an example to get the names of genes that are <5 kb away from
jpayne@68: intergenic SNPs:
jpayne@68: 
jpayne@68: .. code-block:: python
jpayne@68: 
jpayne@68:     from pybedtools import BedTool
jpayne@68: 
jpayne@68:     snps = BedTool('snps.bed.gz')  # [1]
jpayne@68:     genes = BedTool('hg19.gff')    # [1]
jpayne@68: 
jpayne@68:     intergenic_snps = snps.subtract(genes)                       # [2]
jpayne@68:     nearby = genes.closest(intergenic_snps, d=True, stream=True) # [2, 3]
jpayne@68: 
jpayne@68:     for gene in nearby:             # [4]
jpayne@68:         if int(gene[-1]) < 5000:    # [4]
jpayne@68:             print gene.name         # [4]
jpayne@68: 
jpayne@68: Useful features shown here include:
jpayne@68: 
jpayne@68: * `[1]` support for all BEDTools-supported formats (here gzipped BED and GFF)
jpayne@68: * `[2]` wrapping of all BEDTools programs and arguments (here, `subtract` and `closest` and passing
jpayne@68:   the `-d` flag to `closest`);
jpayne@68: * `[3]` streaming results (like Unix pipes, here specified by `stream=True`)
jpayne@68: * `[4]` iterating over results while accessing feature data by index or by attribute
jpayne@68:   access (here `[-1]` and `.name`).
jpayne@68: 
jpayne@68: In contrast, here is the same analysis using shell scripting.  Note that this
jpayne@68: requires knowledge in Perl, bash, and awk.  The run time is identical to the
jpayne@68: `pybedtools` version above:
jpayne@68: 
jpayne@68: .. code-block:: bash
jpayne@68: 
jpayne@68:     snps=snps.bed.gz
jpayne@68:     genes=hg19.gff
jpayne@68:     intergenic_snps=/tmp/intergenic_snps
jpayne@68: 
jpayne@68:     snp_fields=`zcat $snps | awk '(NR == 2){print NF; exit;}'`
jpayne@68:     gene_fields=9
jpayne@68:     distance_field=$(($gene_fields + $snp_fields + 1))
jpayne@68: 
jpayne@68:     intersectBed -a $snps -b $genes -v > $intergenic_snps
jpayne@68: 
jpayne@68:     closestBed -a $genes -b $intergenic_snps -d \
jpayne@68:     | awk '($'$distance_field' < 5000){print $9;}' \
jpayne@68:     | perl -ne 'm/[ID|Name|gene_id]=(.*?);/; print "$1\n"'
jpayne@68: 
jpayne@68:     rm $intergenic_snps
jpayne@68: 
jpayne@68: See the `Shell script comparison <http://daler.github.io/pybedtools/sh-comparison.html>`_ in the docs
jpayne@68: for more details on this comparison, or keep reading the full documentation at
jpayne@68: http://daler.github.io/pybedtools.