allpy: df624c729ab5 utils/freqs.py

allpy

Implemented SequenceCaseMarkup along with the required changes to Monomer.

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Tue, 05 Jul 2011 18:30:42 +0400
parents	7184863832b9
children	aa3cf3b44f86

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

5 import sys

7 sys.stderr.write(__doc__)

9 def freq(monomer):

10 amount = freqs.get(monomer)

11 if amount:

12 return 100.0 * amount / width

13 return ""

15 aln = protein.Alignment().append_file(sys.stdin)

16 monomers = [code1 for code1, modified, _, _ in codes.protein if not modified]

17 monomers += ["-"]

18 width = len(aln.sequences)

19 print ", ".join(map(str, monomers))

20 for column in aln.columns_as_lists():

21 freqs = {}

22 for monomer in column:

23 if monomer:

24 monomer = monomer.code1

25 else:

26 monomer = "-"

27 freqs[monomer] = freqs.get(monomer, 0) + 1

28 print ", ".join(map(str, map(freq, monomers)))