view test/freqs.py @ 432:c4acc245244c
blocks3d/wt improvement
make symbolic link files/resources to wt resoure files
(instead of copy them to files/resources)
author |
boris <bnagaev@gmail.com> |
date |
Tue, 15 Feb 2011 00:07:57 +0300 |
parents |
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children |
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line source
1 """Read alignment on stdin. Print CSV table of letter frequences on stdout.
3 from allpy import protein
4 from allpy.data import codes
7 sys.stderr.write(__doc__)
10 amount = freqs.get(monomer)
12 return 100.0 * amount / width
15 aln = protein.Alignment().append_file(sys.stdin)
16 monomers = [code1 for code1, modified, _, _ in codes.protein if not modified]
18 width = len(aln.sequences)
19 print ", ".join(map(str, monomers))
20 for column in aln.columns_as_lists():
22 for monomer in column:
24 monomer = monomer.code1
27 freqs[monomer] = freqs.get(monomer, 0) + 1
28 print ", ".join(map(str, map(freq, monomers)))