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118 lines
4.0 KiB
Python
118 lines
4.0 KiB
Python
#!/usr/bin/env python
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"""
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Condenses pileup format into ranges of bases.
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usage: %prog [options]
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-i, --input=i: Input pileup file
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-o, --output=o: Output pileup
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-c, --coverage=c: Coverage
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-f, --format=f: Pileup format
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-b, --base=b: Base to select
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-s, --seq_column=s: Sequence column
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-l, --loc_column=l: Base location column
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-r, --base_column=r: Reference base column
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-C, --cvrg_column=C: Coverage column
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"""
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from galaxy import eggs
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import pkg_resources; pkg_resources.require( "bx-python" )
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from bx.cookbook import doc_optparse
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import sys
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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def __main__():
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strout = ''
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#Parse Command Line
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options, args = doc_optparse.parse( __doc__ )
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coverage = int(options.coverage)
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fin = file(options.input, 'r')
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fout = file(options.output, 'w')
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inLine = fin.readline()
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if options.format == 'six':
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seqIndex = 0
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locIndex = 1
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baseIndex = 2
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covIndex = 3
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elif options.format == 'ten':
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seqIndex = 0
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locIndex = 1
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if options.base == 'first':
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baseIndex = 2
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else:
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baseIndex = 3
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covIndex = 7
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else:
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seqIndex = int(options.seq_column) - 1
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locIndex = int(options.loc_column) - 1
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baseIndex = int(options.base_column) - 1
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covIndex = int(options.cvrg_column) - 1
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lastSeq = ''
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lastLoc = -1
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locs = []
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startLoc = -1
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bases = []
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while inLine.strip() != '':
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lineParts = inLine.split('\t')
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try:
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seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex])
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except IndexError, ei:
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if options.format == 'ten':
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stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) )
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else:
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stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) )
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except ValueError, ev:
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if options.format == 'six':
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stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) )
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else:
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stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) )
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# strout += str(startLoc) + '\n'
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# strout += str(bases) + '\n'
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# strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov)
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if loc == lastLoc+1 or lastLoc == -1:
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if cov >= coverage:
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if seq == lastSeq or lastSeq == '':
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if startLoc == -1:
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startLoc = loc
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locs.append(loc)
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bases.append(base)
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else:
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if len(bases) > 0:
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fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
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startLoc = loc
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locs = [loc]
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bases = [base]
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else:
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if len(bases) > 0:
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fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
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startLoc = -1
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locs = []
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bases = []
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else:
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if len(bases) > 0:
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fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
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if cov >= coverage:
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startLoc = loc
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locs = [loc]
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bases = [base]
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else:
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startLoc = -1
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locs = []
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bases = []
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lastSeq = seq
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lastLoc = loc
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inLine = fin.readline()
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if len(bases) > 0:
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fout.write('%s\t%s\t%s\t%s\n' % (lastSeq, startLoc-1, lastLoc, ''.join(bases)))
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fout.close()
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fin.close()
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# import sys
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# strout += file(fout.name,'r').read()
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# sys.stderr.write(strout)
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if __name__ == "__main__" : __main__()
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