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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 with open(input_fname) as in_fh: for line in in_fh: 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) with open(output_fname, 'wb') as out: index.write(out)
if __name__ == "__main__": main()