Source code for galaxy.datatypes.converters.vcf_to_interval_index_converter

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

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() with open(in_file) as in_fh: reader = galaxy_utils.sequence.vcf.Reader(in_fh) 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) with open(out_file, "wb") as out_fh: index.write(out_fh)
if __name__ == "__main__": main()