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Source code for galaxy.datatypes.converters.vcf_to_interval_index_converter

#!/usr/bin/env python
Convert from VCF file to interval index file.
from __future__ import division

import optparse

import galaxy_utils.sequence.vcf
from bx.interval_index_file import Indexes

[docs]def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() in_file, out_file = args # Do conversion. index = Indexes() reader = galaxy_utils.sequence.vcf.Reader(open(in_file)) offset = reader.metadata_len for vcf_line in reader: # VCF format provides a chrom and 1-based position for each variant. # IntervalIndex expects 0-based coordinates. index.add(vcf_line.chrom, vcf_line.pos - 1, vcf_line.pos, offset) offset += len(vcf_line.raw_line) index.write(open(out_file, "w"))
if __name__ == "__main__": main()