Mercurial > repos > vipints > fml_gff3togtf

comparison gtf_to_gff.py @ 5:6e589f267c14

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author devteam
date Tue, 04 Nov 2014 12:15:19 -0500
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4:619e0fcd9126 5:6e589f267c14
1 #!/usr/bin/env python
2 """
3 Convert Gene Transfer Format [GTF] to Generic Feature Format Version 3 [GFF3].
4
5 Usage: python gtf_to_gff.py in.gtf > out.gff3
6
7 Requirement:
8 GFFParser.py: https://github.com/vipints/GFFtools-GX/blob/master/GFFParser.py
9 helper.py : https://github.com/vipints/GFFtools-GX/blob/master/helper.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 import helper
20
21 def GFFWriter(gtf_content):
22 """
23 write the feature information to GFF format
24
25 @args gtf_content: Parsed object from gtf file
26 @type gtf_content: numpy array
27 """
28
29 print '##gff-version 3'
30
31 for ent1 in gtf_content:
32
33 chr_name = ent1['chr']
34 strand = ent1['strand']
35 start = ent1['start']
36 stop = ent1['stop']
37 source = ent1['source']
38 ID = ent1['name']
39 Name = ent1['gene_info']['Name']
40
41 Name = ID if not Name else Name
42
43 print '%s\t%s\tgene\t%d\t%d\t.\t%s\t.\tID=%s;Name=%s' % (chr_name, source, start, stop, strand, ID, Name)
44
45 for idx, tid in enumerate(ent1['transcripts']):
46 print idx
47 print tid
48
49 t_start = ent1['exons'][idx][0][0]
50 t_stop = ent1['exons'][idx][-1][-1]
51 t_type = ent1['transcript_type'][idx]
52
53 utr5_exons, utr3_exons = [], []
54 if ent1['exons'][idx].any() and ent1['cds_exons'][idx].any():
55 utr5_exons, utr3_exons = helper.buildUTR(ent1['cds_exons'][idx], ent1['exons'][idx], strand)
56
57 print '%s\t%s\t%s\t%d\t%d\t.\t%s\t.\tID=%s;Parent=%s' % (chr_name, source, t_type, t_start, t_stop, strand, tid[0], ID)
58
59 for ex_cod in utr5_exons:
60 print '%s\t%s\tfive_prime_UTR\t%d\t%d\t.\t%s\t.\tParent=%s' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0])
61
62 for ex_cod in ent1['cds_exons'][idx]:
63 print '%s\t%s\tCDS\t%d\t%d\t.\t%s\t%d\tParent=%s' % (chr_name, source, ex_cod[0], ex_cod[1], strand, ex_cod[2], tid[0])
64
65 for ex_cod in utr3_exons:
66 print '%s\t%s\tthree_prime_UTR\t%d\t%d\t.\t%s\t.\tParent=%s' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0])
67
68 for ex_cod in ent1['exons'][idx]:
69 print '%s\t%s\texon\t%d\t%d\t.\t%s\t.\tParent=%s' % (chr_name, source, ex_cod[0], ex_cod[1], strand, tid[0])
70
71
72 def __main__():
73
74 try:
75 gtf_fname = sys.argv[1]
76 except:
77 print __doc__
78 sys.exit(-1)
79
80 gtf_file_content = GFFParser.Parse(gtf_fname)
81
82 GFFWriter(gtf_file_content)
83
84 if __name__ == "__main__":
85 __main__()