Mercurial > repos > vipints > fml_gff3togtf

comparison gff_to_gtf.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 Program to convert data from GFF to GTF
4
5 Usage: python gff_to_gtf.py in.gff > out.gtf
6
7 Requirement:
8 GFFParser.py: https://github.com/vipints/GFFtools-GX/blob/master/GFFParser.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 GFFParser
18
19 def printGTF(tinfo):
20 """
21 writing result file in GTF format
22
23 @args tinfo: parsed object from gff file
24 @type tinfo: numpy array
25 """
26
27 for ent1 in tinfo:
28 for idx, tid in enumerate(ent1['transcripts']):
29
30 exons = ent1['exons'][idx]
31 cds_exons = ent1['cds_exons'][idx]
32
33 stop_codon = start_codon = ()
34
35 if ent1['strand'] == '+':
36 if cds_exons.any():
37 start_codon = (cds_exons[0][0], cds_exons[0][0]+2)
38 stop_codon = (cds_exons[-1][1]-2, cds_exons[-1][1])
39 elif ent1['strand'] == '-':
40 if cds_exons.any():
41 start_codon = (cds_exons[-1][1]-2, cds_exons[-1][1])
42 stop_codon = (cds_exons[0][0], cds_exons[0][0]+2)
43 else:
44 print 'STRAND information missing - %s, skip the transcript - %s' % (ent1['strand'], tid[0])
45 pass
46
47 last_cds_cod = 0
48 for idz, ex_cod in enumerate(exons):
49
50 print '%s\t%s\texon\t%d\t%d\t.\t%s\t.\tgene_id "%s"; transcript_id "%s"; exon_number "%d"; gene_name "%s"; ' % (ent1['chr'], ent1['source'], ex_cod[0], ex_cod[1], ent1['strand'], ent1['name'], tid[0], idz+1, ent1['gene_info']['Name'])
51
52 if cds_exons.any():
53 try:
54 print '%s\t%s\tCDS\t%d\t%d\t.\t%s\t%d\tgene_id "%s"; transcript_id "%s"; exon_number "%d"; gene_name "%s"; ' % (ent1['chr'], ent1['source'], cds_exons[idz][0], cds_exons[idz][1], ent1['strand'], cds_exons[idz][2], ent1['name'], tid[0], idz+1, ent1['gene_info']['Name'])
55 last_cds_cod = idz
56 except:
57 pass
58
59 if idz == 0:
60 print '%s\t%s\tstart_codon\t%d\t%d\t.\t%s\t%d\tgene_id "%s"; transcript_id "%s"; exon_number "%d"; gene_name "%s"; ' % (ent1['chr'], ent1['source'], start_codon[0], start_codon[1], ent1['strand'], cds_exons[idz][2], ent1['name'], tid[0], idz+1, ent1['gene_info']['Name'])
61
62 if stop_codon:
63 print '%s\t%s\tstop_codon\t%d\t%d\t.\t%s\t%d\tgene_id "%s"; transcript_id "%s"; exon_number "%d"; gene_name "%s"; ' % (ent1['chr'], ent1['source'], stop_codon[0], stop_codon[1], ent1['strand'], cds_exons[last_cds_cod][2], ent1['name'], tid[0], idz+1, ent1['gene_info']['Name'])
64
65
66 if __name__ == "__main__":
67
68 try:
69 gff_fname = sys.argv[1]
70 except:
71 print __doc__
72 sys.exit(-1)
73
74 Transcriptdb = GFFParser.Parse(gff_fname)
75
76 printGTF(Transcriptdb)