Mercurial > repos > cpt_testbed > cpt_fixaragorn
comparison fix-aragorn-gff3.py @ 0:d8752390c7f7 draft default tip
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author | cpt_testbed |
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date | Fri, 29 Apr 2022 11:32:30 +0000 |
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-1:000000000000 | 0:d8752390c7f7 |
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1 #!/usr/bin/env python | |
2 import sys | |
3 import logging | |
4 import argparse | |
5 from CPT_GFFParser import gffParse, gffWrite, gffSeqFeature | |
6 from Bio.SeqFeature import SeqFeature | |
7 from gff3 import feature_lambda, feature_test_type | |
8 | |
9 logging.basicConfig(level=logging.INFO) | |
10 log = logging.getLogger(__name__) | |
11 | |
12 | |
13 def fixed_feature(rec): | |
14 for idx, feature in enumerate( | |
15 feature_lambda( | |
16 rec.features, feature_test_type, {"types": ["tRNA", "tmRNA"]}, subfeatures=True | |
17 ) | |
18 ): | |
19 | |
20 fid = "%s-%03d" % (feature.type, 1 + idx) | |
21 try: | |
22 name = [feature.type + "-" + feature.qualifiers["Codon"][0]] | |
23 except KeyError: | |
24 name = [feature.qualifiers['product'][0]] | |
25 try: | |
26 origSource = feature.qualifiers["source"][0] | |
27 except: | |
28 origSource = "." | |
29 gene = gffSeqFeature( | |
30 location=feature.location, | |
31 type="gene", | |
32 qualifiers={"ID": [fid + ".gene"], "source": [origSource], "Name": name}, | |
33 ) | |
34 feature.qualifiers["Name"] = name | |
35 # Below that we have an mRNA | |
36 exon = gffSeqFeature( | |
37 location=feature.location, | |
38 type="exon", | |
39 qualifiers={"source": [origSource], "ID": ["%s.exon" % fid], "Name": name}, | |
40 ) | |
41 feature.qualifiers["ID"] = [fid] | |
42 exon.qualifiers["Parent"] = [fid] | |
43 feature.qualifiers["Parent"] = [fid + ".gene"] | |
44 # gene -> trna -> exon | |
45 feature.sub_features = [exon] | |
46 gene.sub_features = [feature] | |
47 yield gene | |
48 | |
49 | |
50 def gff_filter(gff3): | |
51 found_gff = False | |
52 for rec in gffParse(gff3): | |
53 found_gff = True | |
54 rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start) | |
55 rec.annotations = {} | |
56 gffWrite([rec], sys.stdout) | |
57 if not found_gff: | |
58 print("##gff-version 3") | |
59 | |
60 | |
61 if __name__ == "__main__": | |
62 parser = argparse.ArgumentParser(description="add parent gene features to CDSs") | |
63 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations") | |
64 args = parser.parse_args() | |
65 gff_filter(**vars(args)) |