This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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

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()