Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/file/835efa2a8c71/test/usecase2.py
Дата изменения: Unknown
Дата индексирования: Mon Feb 4 05:38:12 2013
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allpy: 835efa2a8c71 test/usecase2.py

allpy

view test/usecase2.py @ 817:835efa2a8c71

optimization of rasmol_homology: keep structure loaded of two sequences only One of steps of this program is superimposition of all sequences with main sequence and saving of all structures to pdb file. Loaded structure of all sequences is not needed to do this. At every moment only structure of main sequence and of superimposing sequence. This optimization results in essential memory saving. Output files should be the same to previous revision. To implement this optimization methods supeimpose and save_pdb of alignment were replaced with methods with same names of sequence. So some code is same as code of methods of alignment. Note: behaves as before, with superimpose and save_pdb methods of alignment. Model was returned by these methods but never used while generating spt script. This can result in collisions of rasmol selections when number of sequences is greater than max number of chains of one model.
author boris (kodomo) <bnagaev@gmail.com>
date Fri, 15 Jul 2011 02:23:27 +0400
parents bed32775625a
children ddf85d0a8924
line source
1 import sys
2 from allpy import dna
3 from allpy.processors import Needle, Left
4 from allpy.fileio import FastaFile
5 from collections import deque
7 width = 15
8 threshold = 10
10 def has_identity(column):
11 as_list = column.values()
12 return len(column) == 2 and as_list[0] == as_list[1]
14 def is_good_window(window):
15 sum_id = sum(int(has_identity(column)) for column in window)
16 return len(window) == width and sum_id >= threshold
18 def find_runs(alignment):
19 window = deque([], width)
20 blocks = []
21 in_block = False
22 for column in alignment.columns:
23 window.append(column)
24 in_block, was_in_block = is_good_window(window), in_block
25 if in_block and not was_in_block:
26 block = dna.Block.from_alignment(alignment, columns=list(window))
27 blocks.append(block)
28 elif in_block:
29 block.columns.append(column)
30 return blocks
32 def blocks_markup(alignment, blocks):
33 for column in alignment.columns:
34 column.in_block = "-"
35 for block in blocks:
36 for column in block.columns:
37 column.in_block = "+"
38 return "".join(column.in_block for column in alignment.columns)
40 def main():
41 alignment = dna.Alignment().append_file(sys.stdin)
42 assert len(alignment.sequences) == 2, "Input must have TWO sequences!"
43 alignment.realign(Left())
44 alignment.realign(Needle())
45 blocks = find_runs(alignment)
47 for n, block in enumerate(blocks, 1):
48 block.to_file(open("block_%02d.fasta" % n, "w"))
50 alignment.to_file(sys.stdout)
51 FastaFile(sys.stdout).write_string(
52 blocks_markup(alignment, blocks),
53 "markup",
54 "In run with window %s and threshold %s" % (width, threshold)
55 )
57 try:
58 main()
59 except Exception, e:
60 print "An error has occured:", e