Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
annotate phylostatistics/phytab_LB_pruner.py @ 0:5b9a38ec4a39 draft default tip
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author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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1 import os |
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2 import optparse |
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3 import subprocess |
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4 from multiprocessing import Pool |
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5 |
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6 directory = "" |
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7 results = "results.data" |
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8 extension = "" |
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9 aligned_extension = ".tab" |
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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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18 "'": '__sq__', |
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19 '"': '__dq__', |
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20 '[': '__ob__', |
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21 ']': '__cb__', |
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22 '{': '__oc__', |
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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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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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133 |
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134 result = [file for file in os.listdir(directory) if file.lower().endswith(aligned_extension)] |
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135 with open(directory + os.sep + results, "a") as f: |
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136 for file in result: |
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137 with open(directory + os.sep + file, "r") as r: |
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138 f.write(toData(r.read(),file)) |
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139 |
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140 if __name__ == '__main__': |
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141 main() |
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142 |