annotate fasta-to-karyotype.py @ 5:a64dc31ab7f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 39a0176dab234a07118a79ac44ca7d79469d3b91"

#!/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],
        )
    )