#!/usr/bin/env python

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

usage: %prog <options> in_file out_file
    -c, --chr-col: chromosome column, default=1
    -s, --start-col: start column, default=2
    -e, --end-col: end column, default=3
"""

from __future__ import division

import optparse
from galaxy import eggs
eggs.require( "bx-python" )
from bx.interval_index_file import Indexes

def main():

    # Read options, args.
    parser = optparse.OptionParser()
    parser.add_option( '-c', '--chr-col', type='int', dest='chrom_col', default=1 )
    parser.add_option( '-s', '--start-col', type='int', dest='start_col', default=2 )
    parser.add_option( '-e', '--end-col', type='int', dest='end_col', default=3 )
    (options, args) = parser.parse_args()
    input_fname, output_fname = args

    # Make column indices 0-based.
    options.chrom_col -= 1
    options.start_col -= 1
    options.end_col -= 1

    # Do conversion.
    index = Indexes()
    offset = 0
    for line in open(input_fname, "r"):
        feature = line.strip().split()
        if not feature or feature[0].startswith("track") or feature[0].startswith("#"):
            offset += len(line)
            continue
        chrom = feature[ options.chrom_col ]
        chrom_start = int( feature[ options.start_col ] )
        chrom_end = int( feature[ options.end_col ] )
        index.add( chrom, chrom_start, chrom_end, offset )
        offset += len(line)

    index.write( open(output_fname, "w") )

if __name__ == "__main__":
    main()