Mercurial > repos > vipints > fml_gff3togtf

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

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Uploaded version 2.0.0 of gfftools ready to import to local instance
author vipints
date Wed, 11 Jun 2014 16:29:25 -0400
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2:db3c67b03d55 3:ff2c2e6f4ab3
1 #!/usr/bin/env python
2 """
3 Convert genome annotation data in a 12 column BED format to GFF3.
4
5 Usage: python bed_to_gff.py in.bed > out.gff
6
7 Requirement:
8 helper.py : https://github.com/vipints/GFFtools-GX/blob/master/helper.py
9
10 Copyright (C)
11 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany.
12 2012-2014 Memorial Sloan Kettering Cancer Center New York City, USA.
13 """
14
15 import re
16 import sys
17 import helper
18
19 def __main__():
20 """
21 main function
22 """
23
24 try:
25 bed_fname = sys.argv[1]
26 except:
27 print __doc__
28 sys.exit(-1)
29
30 bed_fh = helper.open_file(bed_fname)
31
32 for line in bed_fh:
33 line = line.strip( '\n\r' )
34
35 if not line or line[0] in ['#']:
36 continue
37
38 parts = line.split('\t')
39 assert len(parts) >= 12, line
40
41 rstarts = parts[-1].split(',')
42 rstarts.pop() if rstarts[-1] == '' else rstarts
43
44 exon_lens = parts[-2].split(',')
45 exon_lens.pop() if exon_lens[-1] == '' else exon_lens
46
47 if len(rstarts) != len(exon_lens):
48 continue # checking the consistency col 11 and col 12
49
50 if len(rstarts) != int(parts[-3]):
51 continue # checking the number of exons and block count are same
52
53 if not parts[5] in ['+', '-']:
54 parts[5] = '.' # replace the unknown strand with '.'
55
56 # bed2gff result line
57 print '%s\tbed2gff\tgene\t%d\t%s\t%s\t%s\t.\tID=Gene:%s;Name=Gene:%s' % (parts[0], int(parts[1])+1, parts[2], parts[4], parts[5], parts[3], parts[3])
58 print '%s\tbed2gff\ttranscript\t%d\t%s\t%s\t%s\t.\tID=%s;Name=%s;Parent=Gene:%s' % (parts[0], int(parts[1])+1, parts[2], parts[4], parts[5], parts[3], parts[3], parts[3])
59
60 st = int(parts[1])
61 for ex_cnt in range(int(parts[-3])):
62 start = st + int(rstarts[ex_cnt]) + 1
63 stop = start + int(exon_lens[ex_cnt]) - 1
64 print '%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\tParent=%s' % (parts[0], start, stop, parts[4], parts[5], parts[3])
65
66 bed_fh.close()
67
68
69 if __name__ == "__main__":
70 __main__()