allpy: 56d62d405021 test/usecase2.py

allpy

view test/usecase2.py @ 599:56d62d405021

pair_cores_all.py: close openned files to avoid error error "Too many openned files" occured in child processes multiprocessing seems to use old process when new python process is created to avoid increasing of process number. Therefore files openned in childred are not closed automatically

author	boris (kodomo) <bnagaev@gmail.com>
date	Sun, 03 Apr 2011 17:05:32 +0400
parents	0411fa851bba
children	cc1959669928

line source

1 # Fragments are in pair_repeat.fasta

2 from allpy import dna

3 width = 15

4 treshold = 14

6 def my_column_mark(column, threshold):

7 """Helper to mark column (given as dict) by identity."""

8 count = {}

9 for sequence, monomer in column:

10 code = monomer.code1

11 count[code] = count.get(code, 0) + 1

12 for code in count:

13 if count[code] > threshold:

14 return "+"

15 return "-"

17 def my_pair_mark(column):

18 """Helper to mark column of 2 sequences (given as list) by identity."""

19 if column[0] is None or column[1] is None:

20 return "-"

21 if column[0].code1 == column[0].code1:

22 return "+"

23 return "-"

25 def find_runs(markup):

26 """Fund long positive runs.

28 This obscure and probably broken function has nothing to do with allpy,

29 so it's presence in the example is unnecessary.

30 """

31 position = 0

32 count = 0

33 plus_positions=[]

34 for i in range(len(markup)):

35 position += 1

36 if position < width :

37 if markup[i]=="+":

38 count += 1

39 continue

40 if position > width:

41 if markup[i-width] == "+":

42 count -=1

43 if count >= treshold:

44 plus_positions.append(position)

45 if len(plus_positions)==0:

46 raise Exception("No blocks in alignment")

48 blocks=[]

49 start = plus_positions[0]-width + 1

50 stop = plus_positions[0]

51 for p in plus_positions[1:]:

52 if p == stop +1:

53 stop = p

54 continue

55 blocks.append((start,stop))

56 start = p - width + 1

57 stop = p

58 return blocks

60 def main():

61 alignment = dna.Alignment().append_file(open("pair_repeat.fasta"))

62 if len(alignment.sequences) != 2:

63 raise Exception("Input must have exactly 2 sequences!")

64 alignment.realign("needle", gap_open = 0)

65 markup = []

66 for column in alignment.columns_as_lists():

67 markup.append(my_pair_mark(column))

68 markup = alignment.map_columns(my_pair_mark)

69 print find_runs(markup)

71 try:

72 main()

73 except Exception, e:

74 print "An error has occured:", e