Mercurial > repos > vipints > fml_gff3togtf

comparison GFFtools-GX/gff_to_bed.py @ 3:ff2c2e6f4ab3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded version 2.0.0 of gfftools ready to import to local instance
author vipints
date Wed, 11 Jun 2014 16:29:25 -0400
parents
children
comparison
equal deleted inserted replaced
2:db3c67b03d55 3:ff2c2e6f4ab3
1 #!/usr/bin/env python
2 """
3 Convert genome annotation data in GFF/GTF to a 12 column BED format.
4 BED format typically represents the transcript models.
5
6 Usage: python gff_to_bed.py in.gff > out.bed
7
8 Requirement:
9 GFFParser.py: https://github.com/vipints/GFFtools-GX/blob/master/GFFParser.py
10
11 Copyright (C)
12 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany.
13 2012-2014 Memorial Sloan Kettering Cancer Center New York City, USA.
14 """
15
16 import re
17 import sys
18 import GFFParser
19
20 def writeBED(tinfo):
21 """
22 writing result files in bed format
23
24 @args tinfo: list of genes
25 @args tinfo: numpy object
26 """
27
28 for ent1 in tinfo:
29 for idx, tid in enumerate(ent1['transcripts']):
30 exon_cnt = len(ent1['exons'][idx])
31 exon_len = ''
32 exon_cod = ''
33 rel_start = None
34 rel_stop = None
35 for idz, ex_cod in enumerate(ent1['exons'][idx]):#check for exons of corresponding transcript
36 exon_len += '%d,' % (ex_cod[1]-ex_cod[0]+1)
37 if idz == 0: #calculate the relative start position
38 exon_cod += '0,'
39 rel_start = int(ex_cod[0])
40 rel_stop = ex_cod[1]
41 else:
42 exon_cod += '%d,' % (ex_cod[0]-rel_start)
43 rel_stop = int(ex_cod[1])
44
45 if exon_len:
46 score = '0'
47 score = ent1['score'][0] if ent1['score'] else score
48 out_print = [ent1['chr'],
49 str(rel_start),
50 str(rel_stop),
51 tid[0],
52 score,
53 ent1['strand'],
54 str(rel_start),
55 str(rel_stop),
56 '0',
57 str(exon_cnt),
58 exon_len,
59 exon_cod]
60 print '\t'.join(out_print)
61
62 def __main__():
63 try:
64 query_file = sys.argv[1]
65 except:
66 print __doc__
67 sys.exit(-1)
68
69 Transcriptdb = GFFParser.Parse(query_file)
70 writeBED(Transcriptdb)
71
72 if __name__ == "__main__":
73 __main__()