Mercurial > repos > iuc > circos

annotate tiles-from-gff3.py @ 13:8b1cf140bbd4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 0cfd88d16b0b20a66d4b21b037ddee6a8c440d88
author iuc
date Wed, 12 Apr 2023 15:08:23 +0000
parents b84d385679e2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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1 #!/usr/bin/env python
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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2 import logging
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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3 import sys
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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5 from BCBio import GFF
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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7 logging.basicConfig(level=logging.INFO)
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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8 log = logging.getLogger()
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11 if __name__ == "__main__":
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12 attr = sys.argv[2]
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14 for record in GFF.parse(sys.argv[1]):
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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15 if len(record.features) == 0:
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16 continue
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18 for feature in sorted(record.features, key=lambda x: x.location.start):
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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19 # chrom chromStart chromEnd
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20 # name score strand
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21 # thickStart thickEnd itemRgb
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23 kv = {
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24 "strand": 0 if not feature.location.strand else feature.location.strand,
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25 "name": feature.qualifiers.get(attr, ["None"])[0] or feature.id,
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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26 "value": feature.qualifiers.get("score", [0])[0],
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27 "type": feature.type,
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28 }
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30 line = [
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31 record.id,
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32 str(int(feature.location.start)),
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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33 str(int(feature.location.end)),
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34 ",".join(["%s=%s" % x for x in sorted(kv.items())]),
890ef899a3d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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35 ]
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37 sys.stdout.write("\t".join(line))
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38 sys.stdout.write("\n")