view test/usecase3.py @ 1143:a9d4a06ed103
pair-cores/web: add header "Description" before example and description
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1
| author |
Boris Nagaev <bnagaev@gmail.com> |
| date |
Mon, 14 Jan 2013 02:44:43 +0400 |
| parents |
e7d60bf1dfd8 |
| children |
08d892230e8c |
line source
2 from allpy import protein
3 from allpy.processors import Left
4 from allpy.util import open
7 if __name__ == "__main__":
9 infile = open(sys.argv[2])
10 outfile = open(sys.argv[3])
12 # This accepts ranges in form "0:5,7:12,1:-1"
13 ranges = [map(int, range.split(':')) for range in ranges.split(',')]
15 alignment = protein.Alignment().append_file(sys.stdin)
16 for begin, end in ranges:
17 columns = alignment.columns[begin:end]
18 protein.Block.from_alignment(alignment, columns=columns).realign(Left())
19 alignment.remove_gap_columns()
20 alignment.to_file(sys.stdout)
22 # vim: set et ts=4 sts=4 sw=4:
