view test/usecase2.py @ 973:325d165af197
allpy.processors: use NamedTemporaryFile(..., delete=True) in favour of removing the files manually (closes #137)
While writing the relevant line I failed to read the docs properly and was under impression that delete=True refers to the hack, when one creates the file and removes it at once before writing any data to it for the sake of making the file invisible. Which is actually not the case, and the file is removed after being closed.
| author |
Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
| date |
Sat, 25 Feb 2012 20:16:51 +0400 |
| parents |
cc1959669928 |
| children |
08d892230e8c |
line source
3 from collections import deque
5 from allpy.processors import Needle, Left
6 from allpy.fileio import FastaFile
7 from allpy.util import open
11 if __name__ == "__main__":
12 infile = open(sys.argv[1])
13 outfile = open(sys.argv[2])
15 def has_identity(column):
16 as_list = column.values()
17 return len(column) == 2 and as_list[0] == as_list[1]
19 def is_good_window(window):
20 sum_id = sum(int(has_identity(column)) for column in window)
21 return len(window) == width and sum_id >= threshold
23 def find_runs(alignment):
24 window = deque([], width)
27 for column in alignment.columns:
29 in_block, was_in_block = is_good_window(window), in_block
30 if in_block and not was_in_block:
31 block = dna.Block.from_alignment(alignment, columns=list(window))
34 block.columns.append(column)
37 def blocks_markup(alignment, blocks):
38 for column in alignment.columns:
41 for column in block.columns:
43 return "".join(column.in_block for column in alignment.columns)
46 alignment = dna.Alignment().append_file(infile)
47 assert len(alignment.sequences) == 2, "Input must have TWO sequences!"
48 alignment.realign(Left())
49 alignment.realign(Needle())
50 blocks = find_runs(alignment)
52 for n, block in enumerate(blocks, 1):
53 block.to_file(open("block_%02d.fasta" % n, "w"))
55 alignment.to_file(outfile)
56 FastaFile(outfile).write_string(
57 blocks_markup(alignment, blocks),
59 "In run with window %s and threshold %s" % (width, threshold)
65 print "An error has occured:", e
