Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate alignment/phytab_muscle.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:
rev   line source
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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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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8 extension = ".fs"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 aligned_extension = ".afa"
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10
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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 "'": '__sq__',
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 '"': '__dq__',
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 '@': '__at__',
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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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
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43 def toData(text):
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44 text = text.split('\n')
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45 result = ''
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46 for line in text:
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47 if '>' in line:
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48 line = '\n' + line.replace('> ', "") + '\t'
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49 line = line.replace(" ", "\t")
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50 result += line
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51 return result[1:] # Index past the first newline char
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52
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53 def toDataSingle(text):
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54 text = text.split('\n')
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55 result = ''
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56 for line in text:
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57 line = line + '\n'
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58 result += line
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59 return result[1:] # Index past the first newline char
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60
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61 def muscle(input):
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62 file_name = directory + os.sep + input
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63 popen = subprocess.Popen(['muscle', "-in", file_name, "-out", file_name + aligned_extension]) # ./muscle
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64 popen.wait()
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65
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66 popen = subprocess.Popen(['pwd']) # ./muscle
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67 popen.wait()
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68
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69
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70 class Sequence:
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71 def __init__(self, string):
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72 lis = string.split()
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73 self.species = lis[0]
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74 self.family = lis[1]
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75 self.name = lis[2]
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76 self.header = ' '.join(lis[:-1])
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77 self.sequence = lis[-1]
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78 self.string = string
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79
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80 def printFASTA(self):
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81 return '> ' + self.header + '\n' + self.sequence + '\n'
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82
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83
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84 def saveMulti(tabFile):
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85 with open(tabFile) as f:
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86 for line in f:
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87 seq = Sequence(line)
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88 with open(directory + os.sep + seq.family + extension, "a") as p:
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89 p.write(seq.printFASTA())
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90
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91
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92 def saveSingle(fastaFile):
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93 with open(fastaFile) as f:
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94 for line in f:
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95 with open(directory + os.sep + "fasta" + extension, "a") as p:
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96 p.write(line)
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97
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98
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99 def main():
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100 usage = """%prog [options]
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101 options (listed below) default to 'None' if omitted
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102 """
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103 parser = optparse.OptionParser(usage=usage)
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104
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105 parser.add_option(
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106 '-d', '--directory',
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107 metavar="PATH",
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108 dest='path',
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109 default='.',
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110 help='Path to working directory.')
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111
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112 parser.add_option(
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113 '-i', '--in',
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114 dest='input',
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115 action='store',
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116 type='string',
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117 metavar="FILE",
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118 help='Name of input data.')
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119
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120 options, args = parser.parse_args()
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121
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122 global directory
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123 inputFile = unescape(options.input)
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124 directory = unescape(options.path) + os.sep + "data"
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125
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126 os.mkdir(directory)
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127
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128 if isTabular(inputFile):
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129 saveMulti(inputFile)
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130 else:
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131 saveSingle(inputFile)
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132
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133 pool = Pool()
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134 list_of_files = [file for file in os.listdir(directory) if file.lower().endswith(extension)]
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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135 pool.map(muscle, list_of_files)
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136
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137 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>
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138 if isTabular(inputFile):
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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139 with open(directory + os.sep + results, "a") as f:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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140 for file in result:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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141 with open(directory + os.sep + file, "r") as r:
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142 f.write(toData(r.read()) + "\n")
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143 else:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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144 with open(directory + os.sep + results, "a") as f:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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145 for file in result:
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146 with open(directory + os.sep + file, "r") as r:
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147 f.write(toDataSingle(r.read()) + "\n")
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148
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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149 if __name__ == '__main__':
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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150 main()