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+Metadata-Version: 2.1
+Name: pybedtools
+Version: 0.11.0
+Summary: Wrapper around BEDTools for bioinformatics work
+Home-page: https://github.com/daler/pybedtools
+Download-URL: 
+Maintainer: Ryan Dale
+Maintainer-email: ryan.dale@nih.gov
+License: MIT
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+License-File: LICENSE.txt
+Requires-Dist: pysam
+Requires-Dist: numpy
+
+
+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.