Mercurial > repos > bgruening > augustus

annotate extract_features.py @ 5:b3f5d0879dab draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
author iuc
date Thu, 23 May 2019 18:17:05 -0400
parents 4de31938431b
children 09855551d713
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
2
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
3 import argparse
0
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
4 import sys
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
5 import textwrap
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
6
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
7
0
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
8 def main( args ):
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
9 """
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
10 Extract the protein and coding section from an augustus gff, gtf file
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
11 Example file:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
12 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
13 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
14 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
15 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
16 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
17 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
18 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
19 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
20 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
21 # end gene g1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
22 ###
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
23 #
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
24 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
25 #
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
26 # Predicted genes for sequence number 2 on both strands
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
27 # start gene g2
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
28 HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
29 HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
30 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
31 HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
32 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
33 """
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
34 protein_seq = ''
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
35 coding_seq = ''
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
36 if args.protein:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
37 po = open( args.protein, 'w+' )
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
38 if args.codingseq:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
39 co = open( args.codingseq, 'w+' )
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
40
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
41 for line in sys.stdin:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
42 # protein- and coding-sequence are stored as comments
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
43 if line.startswith('#'):
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
44 line = line[2:].strip()
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
45 if line.startswith('start gene'):
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
46 gene_name = line[11:].strip()
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
47
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
48 if protein_seq:
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
49 if line.endswith(']'):
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
50 protein_seq += line[:-1]
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
51 po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
52 protein_seq = ''
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
53 else:
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
54 protein_seq += line
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
55
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
56 if coding_seq:
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
57 if line.endswith(']'):
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
58 coding_seq += line[:-1]
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
59 co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
60 coding_seq = ''
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
61 else:
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
62 coding_seq += line
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
63
0
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
64 if args.protein and line.startswith('protein sequence = ['):
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
65 if line.endswith(']'):
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
66 protein_seq = line[20:-1]
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
67 po.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( protein_seq, 80 ) ) ) )
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
68 protein_seq = ''
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
69 else:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
70 line = line[20:]
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
71 protein_seq = line
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
72
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
73 if args.codingseq and line.startswith('coding sequence = ['):
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
74 if line.endswith(']'):
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
75 coding_seq = line[19:-1]
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
76 co.write( '>%s\n%s\n' % (gene_name, '\n'.join( textwrap.wrap( coding_seq, 80 ) ) ) )
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
77 coding_seq = ''
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
78 else:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
79 line = line[19:]
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
80 coding_seq = line
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
81
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
82 if args.codingseq:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
83 co.close()
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
84 if args.protein:
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
85 po.close()
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
86
4
4de31938431b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
parents: 0
diff changeset
87
0
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
88 if __name__ == '__main__':
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
89 parser = argparse.ArgumentParser()
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
90 parser.add_argument('-p', '--protein', help='Path to the protein file.')
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
91 parser.add_argument('-c', '--codingseq', help='Path to the coding file.')
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
92
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
93 args = parser.parse_args()
af307d3285c5 Uploaded
bgruening
parents:
diff changeset
94 main( args )