view tiles-from-bed.py @ 5:a64dc31ab7f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 39a0176dab234a07118a79ac44ca7d79469d3b91"
author iuc
date Thu, 23 Jan 2020 07:27:22 -0500
parents 014a21767ac4
children
line wrap: on
line source

#!/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["name"] = lineData[3]
                kv["value"] = lineData[4]

            line = [
                lineData[0],  # chrom
                lineData[1],  # chromStart
                lineData[2],  # chromEnd
                ",".join(["%s=%s" % x for x in sorted(kv.items())]),
            ]

            sys.stdout.write("\t".join(line))
            sys.stdout.write("\n")