view additional/glimmer2gff.py @ 6:a07c49839f31

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#!/usr/bin/env python

"""
Input: Glimmer3 prediction
Output: GFF3 file
Return a GFF3 file with the genes predicted by Glimmer3
Bjoern Gruening

Note: Its not a full-fledged GFF3 file, its a really simple one.

"""

import sys, re

def __main__():
    input_file = open(sys.argv[1], 'r')

    print '##gff-version 3\n'
    for line in input_file:
        line = line.strip()
        if line[0] == '>':
            header = line[1:]
        else:
            (id, start, end, frame, score) = re.split('\s+', line)
            if int(end) > int(start):
                strand = '+'
            else:
                strand = '-'
                (start, end) = (end, start)

            rest = 'frame=%s;score=%s' % (frame, score)
            print '\t'.join([header, 'glimmer_prediction', 'predicted_gene', start, end, '.', strand, '.', rest])


if __name__ == "__main__" :
    __main__()