Mercurial > repos > bgruening > antismash
comparison harmonize2antismash.py @ 5:bc88856eddab draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit dc45770442ff516d6f3733e4bdb284be3163de67
| author | bgruening |
|---|---|
| date | Tue, 05 Jul 2022 10:37:38 +0000 |
| parents | |
| children |
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| 4:e78e25d3b4bd | 5:bc88856eddab |
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| 1 #!/usr/bin/env python | |
| 2 import json | |
| 3 import sys | |
| 4 | |
| 5 | |
| 6 output = { | |
| 7 "tool": { | |
| 8 "name": "hAMRonize", | |
| 9 "version": "?", | |
| 10 "description": "Tool for combining results", | |
| 11 "configuration": { | |
| 12 "verbose": "true", "multisetting": ["first", "second"] | |
| 13 }, | |
| 14 }, | |
| 15 "records": [], | |
| 16 } | |
| 17 | |
| 18 with open(sys.argv[1], "r") as handle: | |
| 19 records = json.load(handle) | |
| 20 | |
| 21 for i in records: | |
| 22 start = i["input_gene_start"] | |
| 23 end = i["input_gene_stop"] | |
| 24 label = i["gene_name"] | |
| 25 seqid = i["input_sequence_id"] | |
| 26 | |
| 27 score = i["sequence_identity"] | |
| 28 if start <= end: | |
| 29 fstart = start - 1 | |
| 30 fend = end | |
| 31 else: | |
| 32 fstart = end - 1 | |
| 33 fend = start | |
| 34 | |
| 35 record = { | |
| 36 "name": seqid, | |
| 37 "subregions": [ | |
| 38 { | |
| 39 "start": fstart, | |
| 40 "end": fend, | |
| 41 "label": label, | |
| 42 "details": {"score": str(score)}, | |
| 43 } | |
| 44 ], | |
| 45 } | |
| 46 output["records"].append(record) | |
| 47 | |
| 48 | |
| 49 with open(sys.argv[2], "w") as handle: | |
| 50 json.dump(output, handle, indent=2) |