Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate orthologs/hmmbuild.py @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 import os
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 import optparse
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 import subprocess
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 from multiprocessing import Pool
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5
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6 directory = "./data"
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7 results = "results.data"
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8 extension = ".afa"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 model_extension = ".hmm"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 inputFile = ""
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11 index_of_name_in_hmm = 6
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12
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13
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14 def unescape(string):
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15 mapped_chars = {
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16 '>': '__gt__',
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17 '<': '__lt__',
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18 "'": '__sq__',
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19 '"': '__dq__',
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20 '[': '__ob__',
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 ']': '__cb__',
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 '{': '__oc__',
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 '}': '__cc__',
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24 '@': '__at__',
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25 '\n': '__cn__',
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26 '\r': '__cr__',
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27 '\t': '__tc__',
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28 '#': '__pd__'
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29 }
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30
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31 for key, value in mapped_chars.iteritems():
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32 string = string.replace(value, key)
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33
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34 return string
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35
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36
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37 def toData(text):
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38 lis = text.split()
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39 name = lis[index_of_name_in_hmm]
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40 text = name + "\t" + text.replace("\n", "\\n")
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41 return text
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42
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43
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 def hmmbuild(input):
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45 file_name = directory + os.sep + input
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46 # print file_name
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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47 # return subprocess.Popen(['hmmbuild', "--informat", "afa", file_name + ".hmm", file_name], stdout=subprocess.PIPE).communicate()[0] # ./muscle
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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48 pop = subprocess.Popen(['hmmbuild', "--informat", "afa", file_name + ".hmm", file_name])
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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49 pop.wait()
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50
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51
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52 class Sequence:
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53 def __init__(self, string):
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54 lis = string.split('\t')
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55 # print lis
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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56 self.species = lis[0]
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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57 self.family = lis[1]
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58 self.name = lis[2]
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59 self.header = ' '.join(lis[:-1])
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60 self.sequence = lis[-1]
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61 self.string = string
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62
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63 def printFASTA(self):
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64 return '> ' + self.header + '\n' + self.sequence + '\n'
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65
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66
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67 def main():
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68 usage = """%prog [options]
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69 options (listed below) default to 'None' if omitted
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70 """
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71 parser = optparse.OptionParser(usage=usage)
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72
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73 parser.add_option(
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74 '-i', '--in',
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75 dest='input',
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76 action='store',
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77 type='string',
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78 metavar="FILE",
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79 help='Name of input data.')
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80
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81 options, args = parser.parse_args()
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82
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83 global inputFile, directory
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84 inputFile = unescape(options.input)
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85
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86 os.mkdir(directory)
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87
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88 with open(inputFile) as f:
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89 for line in f:
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90 seq = Sequence(line)
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91 with open(directory + os.sep + seq.family + extension, "a") as p:
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92 p.write(seq.printFASTA())
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93
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94 pool = Pool()
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95 list_of_files = [file for file in os.listdir(directory) if file.lower().endswith(extension)]
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96
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97 pool.map(hmmbuild, list_of_files)
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98
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99 result = [file for file in os.listdir(directory) if file.lower().endswith(model_extension)]
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100 with open(directory + os.sep + results, "a") as f:
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101 for file in result:
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102 with open(directory + os.sep + file, "r") as r:
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103 f.write(toData(r.read()) + "\n")
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104
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105 if __name__ == '__main__':
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106 main()