|
0
|
1 #!/usr/bin/env python
|
|
|
2 """Convert GlimmerHMM GFF3 gene predictions into protein sequences.
|
|
|
3
|
|
|
4 This works with the GlimmerHMM GFF3 output format:
|
|
|
5
|
|
|
6 ##gff-version 3
|
|
|
7 ##sequence-region Contig5.15 1 47390
|
|
|
8 Contig5.15 GlimmerHMM mRNA 323 325 . + . ID=Contig5.15.path1.gene1;Name=Contig5.15.path1.gene1
|
|
|
9 Contig5.15 GlimmerHMM CDS 323 325 . + 0 ID=Contig5.15.cds1.1;Parent=Contig5.15.path1.gene1;Name=Contig5.15.path1.gene1;Note=final-exon
|
|
|
10
|
|
|
11 http://www.cbcb.umd.edu/software/GlimmerHMM/
|
|
|
12
|
|
|
13 Modified version of the converter from Brad Chapman: https://github.com/chapmanb/bcbb/blob/master/biopython/glimmergff_to_proteins.py
|
|
|
14
|
|
|
15 Usage:
|
|
|
16 glimmer_to_proteins.py <glimmer output> <ref fasta> <output file> <convert to protein ... False|True>
|
|
|
17 """
|
|
|
18 import sys
|
|
|
19 import os
|
|
|
20 import operator
|
|
|
21
|
|
|
22 from Bio import SeqIO
|
|
|
23 from Bio.SeqRecord import SeqRecord
|
|
|
24
|
|
|
25 from BCBio import GFF
|
|
|
26
|
|
|
27 def main(glimmer_file, ref_file, out_file, to_protein):
|
|
|
28 with open(ref_file) as in_handle:
|
|
|
29 ref_recs = SeqIO.to_dict(SeqIO.parse(in_handle, "fasta"))
|
|
|
30
|
|
|
31 base, ext = os.path.splitext(glimmer_file)
|
|
|
32
|
|
|
33 with open(out_file, "w") as out_handle:
|
|
|
34 SeqIO.write(protein_recs(glimmer_file, ref_recs, to_protein), out_handle, "fasta")
|
|
|
35
|
|
|
36 def protein_recs(glimmer_file, ref_recs, to_protein):
|
|
|
37 """Generate protein records from GlimmerHMM gene predictions.
|
|
|
38 """
|
|
|
39 with open(glimmer_file) as in_handle:
|
|
|
40 for rec in glimmer_predictions(in_handle, ref_recs):
|
|
|
41 for feature in rec.features:
|
|
|
42 seq_exons = []
|
|
|
43 for cds in feature.sub_features:
|
|
|
44 seq_exons.append(rec.seq[
|
|
|
45 cds.location.nofuzzy_start:
|
|
|
46 cds.location.nofuzzy_end])
|
|
|
47 gene_seq = reduce(operator.add, seq_exons)
|
|
|
48 if feature.strand == -1:
|
|
|
49 gene_seq = gene_seq.reverse_complement()
|
|
|
50
|
|
|
51 if to_protein:
|
|
|
52 yield SeqRecord(gene_seq.translate(), feature.qualifiers["ID"][0], "", "")
|
|
|
53 else:
|
|
|
54 yield SeqRecord(gene_seq, feature.qualifiers["ID"][0], "", "")
|
|
|
55
|
|
|
56 def glimmer_predictions(in_handle, ref_recs):
|
|
|
57 """Parse Glimmer output, generating SeqRecord and SeqFeatures for predictions
|
|
|
58 """
|
|
|
59 for rec in GFF.parse(in_handle, target_lines=1000, base_dict=ref_recs):
|
|
|
60 yield rec
|
|
|
61
|
|
|
62 if __name__ == "__main__":
|
|
|
63 if len(sys.argv) != 3:
|
|
|
64 print __doc__
|
|
|
65 sys.exit()
|
|
|
66 main(*sys.argv[1:])
|
