Mercurial > repos > cpt > cpt_gff_add_parents

comparison cpt_gff_add_parent/gff3_add_parents_to_cds.py @ 0:60651e90119a draft

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author cpt
date Fri, 13 May 2022 04:54:17 +0000
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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 feature in feature_lambda(
15 rec.features, feature_test_type, {"type": "CDS"}, subfeatures=True
16 ):
17 import random
18
19 fid = feature.qualifiers["ID"][0] + "_" + str(random.random())
20 gene = gffSeqFeature(
21 location=feature.location,
22 type="gene",
23 qualifiers={"ID": [fid], "source": ["cpt.fixModel"]},
24 )
25 # Below that we have an mRNA
26 mRNA = gffSeqFeature(
27 location=feature.location,
28 type="mRNA",
29 qualifiers={"source": ["cpt.fixModel"], "ID": ["%s.mRNA" % fid], "Parent": gene.qualifiers["ID"]},
30 )
31 feature.qualifiers["ID"] = [fid + ".CDS"]
32 feature.qualifiers["Parent"] = mRNA.qualifiers["ID"]
33
34 mRNA.sub_features = [feature]
35 gene.sub_features = [mRNA]
36 yield gene
37
38
39 def gff_filter(gff3):
40 for rec in gffParse(gff3):
41 rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start)
42 rec.annotations = {}
43 gffWrite([rec], sys.stdout)
44
45
46 if __name__ == "__main__":
47 parser = argparse.ArgumentParser(description="add parent gene features to CDSs")
48 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
49 args = parser.parse_args()
50 gff_filter(**vars(args))