Mercurial > repos > iuc > circos
view text-from-bed.py @ 6:740057a5126d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
author | iuc |
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date | Fri, 01 May 2020 07:28:50 -0400 |
parents | 014a21767ac4 |
children |
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#!/usr/bin/env python import logging import sys logging.basicConfig(level=logging.INFO) log = logging.getLogger() if __name__ == "__main__": with open(sys.argv[1], "r") as handle: for line in handle: lineData = line.strip().split() # BED3+ chrom chromStart chromEnd # BED6+ name score strand # BED9+ thickStart thickEnd itemRgb kv = {} if len(lineData) >= 6: kv["strand"] = lineData[5].replace("+", "1").replace("-", "-1") kv["value"] = lineData[4] else: sys.exit("Must be BED6+") line = [ lineData[0], # chrom lineData[1], # chromStart lineData[2], # chromEnd lineData[3], ",".join(["%s=%s" % x for x in sorted(kv.items())]), ] sys.stdout.write("\t".join(line)) sys.stdout.write("\n")