Source code for galaxy.datatypes.converters.gff_to_interval_index_converter

#!/usr/bin/env python

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

usage:
    python gff_to_interval_index_converter.py [input] [output]
"""

import fileinput
import sys

from bx.interval_index_file import Indexes
from bx.intervals.io import GenomicInterval

from galaxy.datatypes.util.gff_util import (
    convert_gff_coords_to_bed,
    GFFReaderWrapper,
)


[docs]def main():
    # Arguments
    input_fname, out_fname = sys.argv[1:]

    # Do conversion.
    index = Indexes()
    offset = 0
    reader_wrapper = GFFReaderWrapper(fileinput.FileInput(input_fname), fix_strand=True)
    for feature in list(reader_wrapper):
        # Add feature; index expects BED coordinates.
        if isinstance(feature, GenomicInterval):
            convert_gff_coords_to_bed(feature)
            index.add(feature.chrom, feature.start, feature.end, offset)

        # Always increment offset, even if feature is not an interval and hence
        # not included in the index.
        offset += feature.raw_size

    index.write(open(out_fname, "wb"))


if __name__ == "__main__":
    main()