Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phylostatistics/phytab_LB_pruner.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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0
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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 directory = ""
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 results = "results.data"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 extension = ""
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 aligned_extension = ".tab"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 datatype = ""
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11
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12 perlpath = "/home/galaxy-dist/tools/osiris/tree-manipulation/"
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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 "'": '__sq__',
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 '"': '__dq__',
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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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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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 isTabular(file):
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38 with open(file) as f:
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39 for line in f:
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40 if line[0] == '>':
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41 return False
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42 return True
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43
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44 #def toData(text, name):
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45 # name = name.replace("fasta", "") #file name has fasta when fasta file called
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46 # text = name.replace(".fs.tre", "") + "\t" + text.replace(" " , "")
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47 # return text
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48
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49
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50 def toData(text, name):
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51 text = text.split('\n')
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52 result = ''
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53 for line in text:
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54 if '\t' in line:
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55 line = line.replace("./data/","") + "\n"
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56 result += line
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57 return result # Index past the first newline char
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58
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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59 def LB_pruner(input):
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60 file_name = directory + os.sep + input
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61 popen = subprocess.Popen(['perl', perlpath+'LB_prunerG.pl', file_name, indata, file_name + aligned_extension])
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62 popen.wait()
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63
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64 class Sequence:
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65 def __init__(self, string):
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66 lis = string.split()
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67 self.name = lis[0]
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68 self.tree = lis[1]
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69 self.string = string
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70
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71 def printFASTA(self):
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72 return self.tree + '\n'
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73
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74 def saveMulti(tabFile):
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75 with open(tabFile) as f:
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76 for line in f:
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77 seq = Sequence(line)
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78 with open(directory + os.sep + seq.name + extension, "a") as p:
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79 p.write(seq.printFASTA())
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80
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81 def saveSingle(fastaFile):
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82 with open(fastaFile) as f:
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83 for line in f:
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84 with open(directory + os.sep + "fasta" + extension, "a") as p:
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85 p.write(line)
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86
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87 def main():
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88 usage = """%prog [options]
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89 options (listed below) default to 'None' if omitted
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90 """
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91 parser = optparse.OptionParser(usage=usage)
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92
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93 parser.add_option(
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94 '-d', '--directory',
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95 metavar="PATH",
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96 dest='path',
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97 default='.',
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98 help='Path to working directory.')
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99
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100 parser.add_option(
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101 '-i', '--in',
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102 dest='input',
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103 action='store',
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104 type='string',
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105 metavar="FILE",
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106 help='Name of input data.')
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107
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108 parser.add_option(
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109 '-m', '--mult',
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110 dest='datatype',
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111 action='store',
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112 type='string',
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113 help='Multiplier')
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114
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115 options, args = parser.parse_args()
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116
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117 global directory
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118 global indata
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119 inputFile = unescape(options.input)
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120 directory = unescape(options.path) + os.sep + "data"
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121 indata = unescape(options.datatype)
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122
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123 os.mkdir(directory)
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124
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125 if isTabular(inputFile):
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126 saveMulti(inputFile)
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127 else:
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128 saveSingle(inputFile)
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129
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130 pool = Pool()
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131 list_of_files = [file for file in os.listdir(directory) if file.lower().endswith(extension)]
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132 pool.map(LB_pruner, list_of_files)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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133
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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134 result = [file for file in os.listdir(directory) if file.lower().endswith(aligned_extension)]
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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135 with open(directory + os.sep + results, "a") as f:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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136 for file in result:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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137 with open(directory + os.sep + file, "r") as r:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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138 f.write(toData(r.read(),file))
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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139
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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140 if __name__ == '__main__':
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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141 main()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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142