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galaxy-obo / lib / galaxy / datatypes / converters / gff_to_interval_index_converter.py

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#!/usr/bin/env python

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

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

from __future__ import division

import sys, fileinput
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from galaxy.datatypes.util.gff_util import *
from bx.interval_index_file import Indexes

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, "w") )
    
if __name__ == "__main__": 
    main()