Mercurial > repos > iuc > circos
comparison karyotype-from-fasta.py @ 7:4b519282a05b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
| author | iuc |
|---|---|
| date | Mon, 25 May 2020 10:52:02 -0400 |
| parents | |
| children | e6cbe3190642 |
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| 6:740057a5126d | 7:4b519282a05b |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 import sys | |
| 3 from Bio import SeqIO | |
| 4 | |
| 5 | |
| 6 # Process fasta data, extracting only headers | |
| 7 for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")): | |
| 8 sys.stdout.write( | |
| 9 "chr - {seq_id} {seq_id} 0 {length} chr{idx}color\n".format( | |
| 10 seq_id=seq.id, idx=idx, length=len(seq) | |
| 11 ) | |
| 12 ) |