view fasta-to-karyotype.py @ 6:b84d385679e2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"

#!/usr/bin/env python
import sys

from Bio import SeqIO

# Process fasta data, extracting only headers
for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")):
    sys.stdout.write(
        "chr	-	{seq_id}	{seq_id}	0	{length}	{theme}-{color}\n".format(
            seq_id=seq.id,
            idx=idx,
            length=len(seq),
            color=((idx + 1) % 12),
            theme=sys.argv[2],
        )
    )