view test/usecase2.py @ 645:88c246f20918
Fixed monomer pickling to avoid name clashes. This breaks pickle backwards-compatiblity! [see #35]
Previosly all monomer classes were stored a single namespace,
allpy.data.monomers. This caused a few name clashes, which were mostly
resolved, and one name clash, that was not. (This caused one class to be named
differently depending on the order in which modules were loaded).
Now, instead of one allpy.data.monomers module we have allpy.data.monomers
package with modules dna, rna, protein. This ensures that all name clashes are
resolved uniformly upon any sequence of modules loading.
This may also help in future to keep backward-compatibility longer in case we
replace dynaminc monomer class creation with storing the classes in the module -
if we want to retain independent loading of dna/rna/protein parts.
| author |
Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
| date |
Wed, 08 Jun 2011 21:31:02 +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
