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1 Metadata-Version: 2.1
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2 Name: pybedtools
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3 Version: 0.11.0
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4 Summary: Wrapper around BEDTools for bioinformatics work
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5 Home-page: https://github.com/daler/pybedtools
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6 Download-URL:
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7 Maintainer: Ryan Dale
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8 Maintainer-email: ryan.dale@nih.gov
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9 License: MIT
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10 Classifier: Development Status :: 5 - Production/Stable
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11 Classifier: Intended Audience :: Science/Research
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12 Classifier: License :: OSI Approved :: MIT License
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13 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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14 Classifier: Programming Language :: Python
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15 Classifier: Programming Language :: Python :: 3
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16 Classifier: Programming Language :: Python :: 3.6
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17 Classifier: Programming Language :: Python :: 3.7
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18 Classifier: Programming Language :: Python :: 3.8
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19 Classifier: Topic :: Software Development :: Libraries :: Python Modules
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20 License-File: LICENSE.txt
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21 Requires-Dist: pysam
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22 Requires-Dist: numpy
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23
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24
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25 Overview
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26 --------
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27
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28 .. image:: https://badge.fury.io/py/pybedtools.svg?style=flat
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29 :target: https://badge.fury.io/py/pybedtools
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30
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31 .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg
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32 :target: https://bioconda.github.io
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33
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34 The `BEDTools suite of programs <http://bedtools.readthedocs.org/>`_ is widely
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35 used for genomic interval manipulation or "genome algebra". `pybedtools` wraps
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36 and extends BEDTools and offers feature-level manipulations from within
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37 Python.
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38
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39 See full online documentation, including installation instructions, at
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40 https://daler.github.io/pybedtools/.
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41
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42 The GitHub repo is at https://github.com/daler/pybedtools.
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43
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44 Why `pybedtools`?
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45 -----------------
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46
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47 Here is an example to get the names of genes that are <5 kb away from
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48 intergenic SNPs:
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49
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50 .. code-block:: python
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51
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52 from pybedtools import BedTool
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53
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54 snps = BedTool('snps.bed.gz') # [1]
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55 genes = BedTool('hg19.gff') # [1]
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56
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57 intergenic_snps = snps.subtract(genes) # [2]
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58 nearby = genes.closest(intergenic_snps, d=True, stream=True) # [2, 3]
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59
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60 for gene in nearby: # [4]
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61 if int(gene[-1]) < 5000: # [4]
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62 print gene.name # [4]
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63
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64 Useful features shown here include:
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65
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66 * `[1]` support for all BEDTools-supported formats (here gzipped BED and GFF)
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67 * `[2]` wrapping of all BEDTools programs and arguments (here, `subtract` and `closest` and passing
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68 the `-d` flag to `closest`);
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69 * `[3]` streaming results (like Unix pipes, here specified by `stream=True`)
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70 * `[4]` iterating over results while accessing feature data by index or by attribute
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71 access (here `[-1]` and `.name`).
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72
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73 In contrast, here is the same analysis using shell scripting. Note that this
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74 requires knowledge in Perl, bash, and awk. The run time is identical to the
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75 `pybedtools` version above:
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76
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77 .. code-block:: bash
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78
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79 snps=snps.bed.gz
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80 genes=hg19.gff
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81 intergenic_snps=/tmp/intergenic_snps
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82
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83 snp_fields=`zcat $snps | awk '(NR == 2){print NF; exit;}'`
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84 gene_fields=9
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85 distance_field=$(($gene_fields + $snp_fields + 1))
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86
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87 intersectBed -a $snps -b $genes -v > $intergenic_snps
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88
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89 closestBed -a $genes -b $intergenic_snps -d \
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90 | awk '($'$distance_field' < 5000){print $9;}' \
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91 | perl -ne 'm/[ID|Name|gene_id]=(.*?);/; print "$1\n"'
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92
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93 rm $intergenic_snps
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94
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95 See the `Shell script comparison <http://daler.github.io/pybedtools/sh-comparison.html>`_ in the docs
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96 for more details on this comparison, or keep reading the full documentation at
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97 http://daler.github.io/pybedtools.
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