Mercurial > repos > bjoern-gruening > glimmer3

comparison glimmer3/glimmer2gff.py @ 0:e11e303c39a4 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bjoern-gruening
date Wed, 11 Jan 2012 09:34:45 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:e11e303c39a4
1 #!/usr/bin/env python
2
3 """
4 Input: Glimmer3 prediction
5 Output: GFF3 file
6 Return a GFF3 file with the genes predicted by Glimmer3
7 Bjoern Gruening
8
9 Note: Its not a full-fledged GFF3 file, its a really simple one.
10
11 """
12
13 import sys, re
14
15 def __main__():
16 input_file = open(sys.argv[1], 'r')
17
18 print '##gff-version 3\n'
19 for line in input_file:
20 line = line.strip()
21 if line[0] == '>':
22 header = line[1:]
23 else:
24 (id, start, end, frame, score) = re.split('\s+', line)
25 if int(end) > int(start):
26 strand = '+'
27 else:
28 strand = '-'
29 (start, end) = (end, start)
30
31 rest = 'frame=%s;score=%s' % (frame, score)
32 print '\t'.join([header, 'glimmer_prediction', 'predicted_gene', start, end, '.', strand, '.', rest])
33
34
35 if __name__ == "__main__" :
36 __main__()