Mercurial > repos > iuc > circos

comparison text-from-gff3.py @ 2:014a21767ac4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:57 -0400
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1:ae9994cf526f 2:014a21767ac4
1 #!/usr/bin/env python
2 import logging
3 import sys
4
5 from BCBio import GFF
6
7 logging.basicConfig(level=logging.INFO)
8 log = logging.getLogger()
9
10
11 if __name__ == "__main__":
12 attr = sys.argv[2]
13
14 for record in GFF.parse(sys.argv[1]):
15 if len(record.features) == 0:
16 continue
17
18 for feature in sorted(record.features, key=lambda x: x.location.start):
19 # chrom chromStart chromEnd
20 # name score strand
21 # thickStart thickEnd itemRgb
22
23 kv = {
24 "strand": 0 if not feature.location.strand else feature.location.strand,
25 "value": feature.qualifiers.get("score", [0])[0],
26 }
27
28 if attr not in feature.qualifiers:
29 continue
30
31 name = feature.qualifiers[attr][0]
32
33 line = [
34 record.id,
35 str(int(feature.location.start)),
36 str(int(feature.location.end)),
37 name,
38 ",".join(["%s=%s" % x for x in sorted(kv.items())]),
39 ]
40
41 sys.stdout.write("\t".join(line))
42 sys.stdout.write("\n")