Mercurial > repos > bgruening > antismash
diff 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 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/harmonize2antismash.py Tue Jul 05 10:37:38 2022 +0000 @@ -0,0 +1,50 @@ +#!/usr/bin/env python +import json +import sys + + +output = { + "tool": { + "name": "hAMRonize", + "version": "?", + "description": "Tool for combining results", + "configuration": { + "verbose": "true", "multisetting": ["first", "second"] + }, + }, + "records": [], +} + +with open(sys.argv[1], "r") as handle: + records = json.load(handle) + + for i in records: + start = i["input_gene_start"] + end = i["input_gene_stop"] + label = i["gene_name"] + seqid = i["input_sequence_id"] + + score = i["sequence_identity"] + if start <= end: + fstart = start - 1 + fend = end + else: + fstart = end - 1 + fend = start + + record = { + "name": seqid, + "subregions": [ + { + "start": fstart, + "end": fend, + "label": label, + "details": {"score": str(score)}, + } + ], + } + output["records"].append(record) + + +with open(sys.argv[2], "w") as handle: + json.dump(output, handle, indent=2)