galaxy-obo / lib / galaxy / datatypes / converters /

The default branch has multiple heads

Full commit
#!/usr/bin/env python

Convert from GFF file to interval index file.

    python [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__":