Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
annotate phylogenies/phytab_clearcut.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 = ".fs" |
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9 aligned_extension = ".tre" |
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10 datatype = "" |
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11 |
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12 def unescape(string): |
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13 mapped_chars = { |
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14 '>': '__gt__', |
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15 '<': '__lt__', |
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16 "'": '__sq__', |
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17 '"': '__dq__', |
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18 '[': '__ob__', |
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19 ']': '__cb__', |
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20 '{': '__oc__', |
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21 '}': '__cc__', |
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22 '@': '__at__', |
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23 '\n': '__cn__', |
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24 '\r': '__cr__', |
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25 '\t': '__tc__', |
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26 '#': '__pd__' |
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27 } |
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28 |
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29 for key, value in mapped_chars.iteritems(): |
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30 string = string.replace(value, key) |
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31 |
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32 return string |
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33 |
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34 |
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35 def isTabular(file): |
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36 with open(file) as f: |
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37 for line in f: |
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38 if line[0] == '>': |
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39 return False |
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40 return True |
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41 |
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42 def toData(text, name): |
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43 name = name.replace("fasta", "") #file name has fasta when fasta file called |
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44 text = name.replace(".fs.tre", "") + "\t" + text.replace(" " , "") |
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45 return text |
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46 |
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47 # |
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48 #def toData(text): |
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49 # text = text.split('\n') |
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50 # result = '' |
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51 # for line in text: |
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52 # if '>' in line: |
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53 # line = '\n' + line.replace('>', "") + '\t' |
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54 # line = line.replace(" ", "\t") |
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55 # result += line |
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56 # return result[1:] # Index past the first newline char |
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57 |
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58 def clearcut(input): |
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59 file_name = directory + os.sep + input |
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60 popen = subprocess.Popen(['clearcut', "--in=" + file_name, "--out="+file_name + aligned_extension, "--alignment","-k", indata]) |
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61 popen.wait() |
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62 |
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63 class Sequence: |
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64 def __init__(self, string): |
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65 lis = string.split() |
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66 self.species = lis[0] |
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67 self.family = lis[1] |
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68 self.name = lis[2] |
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69 self.header = ' '.join(lis[:-1]) |
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70 self.sequence = lis[-1] |
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71 self.string = string |
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72 |
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73 def printFASTA(self): |
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74 return '>' + self.header + '\n' + self.sequence + '\n' |
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75 |
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76 def saveMulti(tabFile): |
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77 with open(tabFile) as f: |
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78 for line in f: |
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79 seq = Sequence(line) |
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80 with open(directory + os.sep + seq.family + extension, "a") as p: |
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81 p.write(seq.printFASTA()) |
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82 |
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83 def saveSingle(fastaFile): |
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84 with open(fastaFile) as f: |
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85 for line in f: |
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86 with open(directory + os.sep + "fasta" + extension, "a") as p: |
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87 p.write(line) |
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88 |
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89 def main(): |
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90 usage = """%prog [options] |
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91 options (listed below) default to 'None' if omitted |
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92 """ |
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93 parser = optparse.OptionParser(usage=usage) |
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94 |
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95 parser.add_option( |
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96 '-d', '--directory', |
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97 metavar="PATH", |
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98 dest='path', |
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99 default='.', |
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100 help='Path to working directory.') |
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101 |
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102 parser.add_option( |
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103 '-i', '--in', |
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104 dest='input', |
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105 action='store', |
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106 type='string', |
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107 metavar="FILE", |
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108 help='Name of input data.') |
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109 |
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110 parser.add_option( |
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111 '-t', '--type', |
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112 dest='datatype', |
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113 action='store', |
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114 type='string', |
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115 help='-P for protein. -D for DNA.') |
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116 |
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117 options, args = parser.parse_args() |
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118 |
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119 global directory |
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120 global indata |
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121 inputFile = unescape(options.input) |
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122 directory = unescape(options.path) + os.sep + "data" |
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123 indata = "-" + unescape(options.datatype) |
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124 |
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125 os.mkdir(directory) |
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126 |
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127 if isTabular(inputFile): |
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128 saveMulti(inputFile) |
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129 else: |
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130 saveSingle(inputFile) |
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131 |
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132 pool = Pool() |
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133 list_of_files = [file for file in os.listdir(directory) if file.lower().endswith(extension)] |
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134 pool.map(clearcut, list_of_files) |
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135 |
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136 result = [file for file in os.listdir(directory) if file.lower().endswith(aligned_extension)] |
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137 with open(directory + os.sep + results, "a") as f: |
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138 for file in result: |
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139 with open(directory + os.sep + file, "r") as r: |
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140 f.write(toData(r.read(),file)) |
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141 |
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142 if __name__ == '__main__': |
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143 main() |