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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
"""
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()