allpy: 679494ad2f4e test/usecase3.py

allpy

view test/usecase3.py @ 336:679494ad2f4e

MSF output format by request implemented

author	Andrei <aba@belozersky.msu.ru>
date	Wed, 12 Jan 2011 20:23:22 +0300
parents	38888b46c342
children	20944c113ea3

line source

1 from allpy import protein

2 import sys

3 import optparse

5 if len(sys.argv)==1:

6 print("usercase3 shisfts left all letters in specified vertical block of input alignment")

7 print("\n Use python usercase3.py -h for help")

8 exit()

10 parser = optparse.OptionParser()

12 parser.add_option("-i", "--in-file", help="Input alignment in fasta format", dest="in_file")

13 parser.add_option("-o", "--out-file", help="Output refined alignment in fasta format", dest="out_file", default='result.fasta')

14 parser.add_option("-f", "--_from", help="First position of refining block", dest="_from")

15 parser.add_option("-t", "--to", help="Last position of refining block", dest="to")

17 options, args = parser.parse_args()

18 in_file = options.in_file

19 out_file = options.out_file

20 _from = options._from

21 to = options.to

24 if in_file==None or _from==None or to==None:

25 print("Missed command line parameters.")

26 print("Use python usercase3.py -h for help")

27 exit()

29 try:

30 f = open(in_file)

31 except:

32 print("File %s was not found" % in_file)

33 exit()

35 try:

36 ifrom = int(_from)

37 ito = int(to)

38 except:

39 print("Values -f %s and -t %s must be interer!" % (_from,to))

40 exit()

42 alignment = protein.Alignment.from_fasta(open(in_file))

44 alignment.length = len(alignment.columns)

46 if ito >= alignment.length:

47 print("to must be smaller than alignment length!")

48 exit()

50 if ifrom >= ito :

51 print("from must be greater than to!")

52 exit()

55 conservative = []

56 if ifrom > 1:

57 conservative.append((0,int(_from)))

58 if ito < alignment.length:

59 conservative.append((ito,alignment.length-1))

61 print conservative

63 #conservative = [(10,20), (40,50)]

64 #conservative = [(0,6),(18,37)]

66 def ranges_to_markup(ranges):

67 """Convert list of ranges to line of markup.

69 This has nothing to do with allpy.

70 """

71 markup = ["-"] * len(alignment.columns)

72 for begin, end in ranges:

73 for i in range(begin, end+1):

74 markup[i] = "+"

75 return "".join(markup)

77 def markup_to_blocks(markup):

78 """Convert markup line to a bunch of blocks, one for each sequential run."""

79 current = None

80 blocks = {}

81 for mark, column in zip(markup, alignment.columns):

82 if mark != current:

83 block = protein.Block.from_alignment(alignment, columns=[])

84 blocks[mark] = blocks.get(mark, []) + [block]

85 current = mark

86 blocks[mark][-1].columns.append(column)

87 return blocks

89 def main():

90 markup = ranges_to_markup(conservative)

91 blocks = markup_to_blocks(markup)

92 for block in blocks["-"]:

93 block.flush_left()

94 alignment.to_fasta(open(out_file, "w"))

96 main()