Mercurial > repos > iuc > circos

annotate karyotype-from-fasta.py @ 8:b7c1698df177 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit cc96dd4a8aef7d0b6d3057024af0344ab8a9410f"
author iuc
date Fri, 12 Jun 2020 14:39:23 +0000
parents ecaa0210e62b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
2 import sys
8
b7c1698df177 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit cc96dd4a8aef7d0b6d3057024af0344ab8a9410f"
iuc
parents: 7
diff changeset
3
7
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
4 from Bio import SeqIO
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
5
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
6
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
7 # Process fasta data, extracting only headers
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
8 for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")):
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
9 sys.stdout.write(
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
10 "chr - {seq_id} {seq_id} 0 {length} chr{idx}color\n".format(
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
11 seq_id=seq.id, idx=idx, length=len(seq)
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
12 )
ecaa0210e62b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit ef20b4968a6d00c49209de6b723f8b96d8bd128a"
iuc
parents:
diff changeset
13 )