Mercurial > repos > cpt > cpt_fix_sixpack

comparison gff3_fix_sixpack.py @ 3:efa4dfc23549 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:42:28 +0000
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2:6a9b026cb378 3:efa4dfc23549
1 #!/usr/bin/env python
2 import sys
3 import logging
4 import argparse
5 from CPT_GFFParser import gffParse, gffWrite
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 # Get all gene features to remove the mRNAs from
15 for feature in feature_lambda(
16 rec.features, feature_test_type, {"type": "gene"}, subfeatures=True
17 ):
18 gene = feature
19 sub_features = []
20 # Filter out mRNA subfeatures, save other ones to new gene object.
21 for sf in feature_lambda(
22 feature.sub_features,
23 feature_test_type,
24 {"type": "mRNA"},
25 subfeatures=True,
26 invert=True,
27 ):
28 sf.qualifiers["Parent"] = gene.qualifiers["ID"]
29 sub_features.append(sf)
30 # override original subfeatures with our filtered list
31 gene.sub_features = sub_features
32 yield gene
33
34
35 def gff_filter(gff3):
36 for rec in gffParse(gff3):
37 rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start)
38 rec.annotations = {}
39 gffWrite([rec], sys.stdout)
40
41
42 if __name__ == "__main__":
43 parser = argparse.ArgumentParser(description="Fix gene model from naive ORF caller")
44 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
45 args = parser.parse_args()
46 gff_filter(**vars(args))