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#!/usr/bin/env python3
# encoding: utf-8
"""
makeBashScripts.py
"""
import sys
import os
def main():
tool_map = {'annotate': 'annotateBed',
'bamtobed': 'bamToBed',
'bamtofastq': 'bamToFastq',
'bed12tobed6': 'bed12ToBed6',
'bedpetobam': 'bedpeToBam',
'bedtobam': 'bedToBam',
'closest': 'closestBed',
'cluster': 'clusterBed',
'complement': 'complementBed',
'coverage': 'coverageBed',
'expand': 'expandCols',
'flank': 'flankBed',
'genomecov': 'genomeCoverageBed',
'getfasta': 'fastaFromBed',
'groupby': 'groupBy',
'igv': 'bedToIgv',
'intersect': 'intersectBed',
'links': 'linksBed',
'map': 'mapBed',
'maskfasta': 'maskFastaFromBed',
'merge': 'mergeBed',
'multicov': 'multiBamCov',
'multiinter': 'multiIntersectBed',
'nuc': 'nucBed',
'overlap': 'getOverlap',
'pairtobed': 'pairToBed',
'pairtopair': 'pairToPair',
'random': 'randomBed',
'shift': 'shiftBed',
'shuffle': 'shuffleBed',
'slop': 'slopBed',
'sort': 'sortBed',
'subtract': 'subtractBed',
'tag': 'tagBam',
'unionbedg': 'unionBedGraphs',
'window': 'windowBed',
'makewindows': 'windowMaker'}
# create a BASH script for each old tool, mapping to the new CLI command.
for tool in tool_map:
new = tool
old = tool_map[tool]
script = open('bin/' + old, 'w')
script.write("#!/bin/sh\n")
script.write("${0%/*}/bedtools " + new + " \"$@\"\n")
script.close()
if __name__ == "__main__":
main()
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