root/galaxy-central/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py @ 2

#!/usr/bin/env python

"""
Convert from VCF file to interval index file.
"""

from __future__ import division

import optparse
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import galaxy_utils.sequence.vcf
from bx.interval_index_file import Indexes

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()