allpy: b556c96c6719 utils/make

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view utils/make_homologies.py @ 1168:b556c96c6719

blocks3d/www Makefile: never check certificates of github, they are too confusing for wget

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Mon, 26 May 2014 17:20:29 +0400
parents	3312472eb920
children

line source

1 #!/usr/bin/python

2 import sys

3 from glob import glob

4 import optparse

5 from allpy import protein

6 from allpy.homology import MonomerHomology

7 from allpy import markups

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

12 print("Makes homology files from (case sensitive by request) input alignments")

13 print("Type 'python make_homologies.py -h' for parameters")

14 exit()

16 parser = optparse.OptionParser()

18 parser.add_option("-c", "--case", action="store_true", help="Case sensitive interpretation of input alignment (False if -c missed)", dest="case")

19 parser.add_option("-n", "--file_names", help="File with alignment fasta files names", dest="file_names")

20 parser.add_option("-g", "--files-glob", help="Glob expression for alignment file names")

22 parser.add_option("-d", "--base_in", help="Name of directory with alignment files (default=\"\")", dest="base_in", default="")

23 parser.add_option("-s", "--suffix", help="Suffix for out files", dest="suffix", default = "hom")

24 parser.add_option("-o", "--base_out", help="Name of directory for outfiles (default=\"\")", dest="base_out", default="")

25 parser.add_option("-f", "--format", help="Format of input file: 'markup' or 'fasta' (default)", dest="format", default = "fasta")

28 # FOR ONE INPUT ALIGNMENT

29 #parser.add_option("-i", "--in_file", help="File with an alignment in fasta", dest="in_file")

30 #parser.add_option("-o", "--result", help="Output file with monomer homology classes (default: result.xls)", dest="out_file", default = "result.xls")

32 options, args = parser.parse_args()

33 vars().update(vars(options))

35 if files_glob:

36 alignment_names = glob(files_glob)

38 else:

40 try:

41 f = open(file_names)

42 except:

43 raise Exception("File %s does not exists! Use python make_homologies.py -h for parameters" % file_names)

45 alignment_names = []

46 for line in f:

47 line = line.strip()

48 if len(line) == 0:

49 continue

50 line = line.strip().split("#")[0]

51 if len(line) == 0:

52 continue

53 alignment_names.append(line.split()[0])

56 if len(base_in) > 0:

57 if base_in[-1]!= "/":

58 base_in = base_in + "/"

60 if len(base_out) > 0:

61 if base_out[-1]!= "/":

62 base_out = base_out + "/"

65 print("Wait...")

67 for alignment_name in alignment_names:

68 in_file_name = base_in + alignment_name

69 out_file_name = base_out + alignment_name.partition(".fasta")[0] + ".xls"

71 classes_number = MonomerHomology.case_homology(in_file_name,out_file_name, case, format)

72 print ("File %s: %s monomer homology classes stored" % (out_file_name,classes_number))

74 print("...Done")

78 # vim: set et ts=4 sts=4 sw=4: