Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate alignment/phytab_ssr.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 #!/usr/bin/env python
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2
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3 import os
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4 import optparse
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5 import subprocess
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6 from multiprocessing import Pool
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7 from functools import partial
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8
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9 directory = ""
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10 results = "results.data"
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11 extension = ".fs"
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12 slim_extension = ".slim"
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13 jarpath='/home/galaxy/pkgs/SSR/SimilarSequenceRemover.jar'
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14
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15 def unescape(string):
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16 mapped_chars = {
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17 '>': '__gt__',
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18 '<': '__lt__',
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19 "'": '__sq__',
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20 '"': '__dq__',
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21 '[': '__ob__',
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22 ']': '__cb__',
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23 '{': '__oc__',
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24 '}': '__cc__',
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25 '@': '__at__',
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26 '\n': '__cn__',
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27 '\r': '__cr__',
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28 '\t': '__tc__',
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29 '#': '__pd__'
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30 }
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31
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32 for key, value in mapped_chars.iteritems():
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33 string = string.replace(value, key)
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34
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35 return string
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36
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37
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38 def isTabular(file):
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39 with open(file) as f:
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40 for line in f:
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41 if line[0] == '>':
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42 return False
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43 return True
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44
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45
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46 def toData(text):
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47 text = text.split('\n')
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48 result = ''
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49 for line in text:
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50 if '>' in line:
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51 line = '\n' + line.replace('> ', "") + '\t'
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52 line = line.replace(" ", "\t")
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53 result += line
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54 return result[1:] # Index past the first newline char
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55
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56 def toDataSingle(text):
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57 text = text.split('\n')
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58 result = ''
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59 for line in text:
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60 line = line + '\n'
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61 result += line
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62 return result[1:] # Index past the first newline char
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63
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64 def runSimilarSequenceRemover(input):
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65 input_name = directory + os.sep + input
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66 outfasta = input_name + slim_extension
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67 call = subprocess.call(['java','-jar', jarpath, '-i', input_name, '-o', outfasta, 's=' + percentage, '-h', alignallornot ])
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68
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69 class Sequence:
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70 def __init__(self, string):
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71 lis = string.split()
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72 self.species = lis[0]
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73 self.family = lis[1]
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74 self.name = lis[2]
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75 self.header = ' '.join(lis[:-1])
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76 self.sequence = lis[-1]
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77 self.string = string
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78
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79 def printFASTA(self):
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80 return '> ' + self.header + '\n' + self.sequence + '\n'
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81
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82
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83 def saveMulti(tabFile):
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84 with open(tabFile) as f:
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85 for line in f:
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86 seq = Sequence(line)
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87 with open(directory + os.sep + seq.family + extension, "a") as p:
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88 p.write(seq.printFASTA())
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89
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90
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91 def saveSingle(fastaFile):
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92 with open(fastaFile) as f:
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93 for line in f:
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94 with open(directory + os.sep + "fasta" + extension, "a") as p:
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95 p.write(line)
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96
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97
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98 def main():
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99 usage = """%prog [options]
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100 options (listed below) default to 'None' if omitted
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101 """
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102 parser = optparse.OptionParser(usage=usage)
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103
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104 parser.add_option(
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105 '-d', '--directory',
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106 metavar="PATH",
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107 dest='path',
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108 default='.',
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109 help='Path to working directory.')
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110
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111 parser.add_option(
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112 '-i', '--in',
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113 dest='input',
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114 action='store',
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115 type='string',
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116 metavar="FILE",
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117 help='Name of input data.')
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118
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119 parser.add_option(
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120 '-a', '--alignall',
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121 dest='alignall',
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122 action='store',
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123 type='string', help='t or f. t only aligns first 100 sites instead of entire seq')
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124
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125 parser.add_option(
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126 '-s', '--similarity',
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127 dest='similarity',
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128 action='store',
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129 type='float',
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130 help='Percentage similarity as cutoff (eg 0.99).')
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131
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132 options, args = parser.parse_args()
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133
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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134 global directory
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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135 global percentage
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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136 global alignallornot
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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137 inputFile = unescape(options.input)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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138 directory = unescape(options.path) + os.sep + "data"
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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139 percentage = str(options.similarity)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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140 alignallornot = options.alignall
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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141
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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142 os.mkdir(directory)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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143
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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144 if isTabular(inputFile):
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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145 saveMulti(inputFile)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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146 else:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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147 saveSingle(inputFile)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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148
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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149 pool = Pool()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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150 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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151 list_of_files = sorted(list_of_files)
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152
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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153 pool.map(runSimilarSequenceRemover, list_of_files)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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154
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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155 result = [file for file in os.listdir(directory) if file.lower().endswith(slim_extension)]
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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156 if isTabular(inputFile):
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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157 with open(directory + os.sep + results, "a") as f:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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158 for file in result:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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159 with open(directory + os.sep + file, "r") as r:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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160 f.write(toData(r.read()) + "\n")
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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161 else:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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162 with open(directory + os.sep + results, "a") as f:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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163 for file in result:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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164 with open(directory + os.sep + file, "r") as r:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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165 f.write(r.read() +'\n')
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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166
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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167 if __name__ == '__main__':
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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168 main()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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169
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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170