Mercurial > repos > iuc > circos
diff genome-lengths-to-karyotype.py @ 2:014a21767ac4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author | iuc |
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date | Tue, 17 Sep 2019 16:54:57 -0400 |
parents | |
children | 740057a5126d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genome-lengths-to-karyotype.py Tue Sep 17 16:54:57 2019 -0400 @@ -0,0 +1,25 @@ +#!/usr/bin/env python +import csv +import sys + + +idx = 0 +with open(sys.argv[1], "r") as csvfile: + spamreader = csv.reader(csvfile, delimiter="\t", quotechar='"') + for row in spamreader: + if len(row) < 2: + continue + + seq_id = row[0] + length = row[1] + + sys.stdout.write( + "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format( + seq_id=seq_id, + idx=idx, + length=length, + color=((idx + 1) % 12), + theme=sys.argv[2], + ) + ) + idx += 1