view karyotype-from-fasta.py @ 11:0ee66defe58b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473"

#!/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}	chr{idx}color\n".format(
            seq_id=seq.id, idx=idx, length=len(seq)
        )
    )