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Source code for galaxy.datatypes.converters.pileup_to_interval_index_converter

#!/usr/bin/env python

"""
Convert from pileup file to interval index file.

usage: %prog <options> in_file out_file
"""
from __future__ import division

import optparse

from bx.interval_index_file import Indexes


[docs]def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args # Do conversion. index = Indexes() offset = 0 for line in open( input_fname, "r" ): chrom, start = line.split()[ 0:2 ] # Pileup format is 1-based. start = int( start ) - 1 index.add( chrom, start, start + 1, offset ) offset += len( line ) index.write( open(output_fname, "w") )
if __name__ == "__main__": main()