view test/usecase2.py @ 816:d137df18a8bf
structure: create method superimpose of SequenceMixin
Most of code of AlignmentMixin.superimpose was moved to SequenceMixin.
Structures of sequences can be superimposed manually (in custom order,
or with additions action such as loading/unloading of structure).
| author |
boris (kodomo) <bnagaev@gmail.com> |
| date |
Fri, 15 Jul 2011 02:06:23 +0400 |
| parents |
bed32775625a |
| children |
ddf85d0a8924 |
line source
3 from allpy.processors import Needle, Left
4 from allpy.fileio import FastaFile
5 from collections import deque
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)
22 for column in alignment.columns:
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))
29 block.columns.append(column)
32 def blocks_markup(alignment, blocks):
33 for column in alignment.columns:
36 for column in block.columns:
38 return "".join(column.in_block for column in alignment.columns)
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),
54 "In run with window %s and threshold %s" % (width, threshold)
60 print "An error has occured:", e
