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1 #!/SATA/bioinfo/galaxy/galaxy_env/bin/python
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2
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3 '''
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4 Created on Jan 1, 2011
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5
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6 @author: John L. Herndon
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7 @contact: herndon@cs.colostate.edu
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8 @organization: Colorado State University
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9 @group: Computer Science Department, Asa Ben-Hur's laboratory
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10 Mau added the -o primerOutfile -l logfile option
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11 '''
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12
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13 import exceptions
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14 import sys
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15 import time
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16
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17 import getopt
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18 from primertools import *
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19
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20 version="0.5.0"
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21
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22
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23 class UniqPrimerFinder( object ):
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24
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25 def __init__( self, includeFiles, excludeFiles, crossValidate, eprimerOptions):
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26
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27 utils.logMessage( "UniqPrimerFinder::__init__()", "Initializing UniqPrimerFinder" )
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28 self.includeFiles = includeFiles
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29 self.includeFileManager = includefilemanager.IncludeFileManager( )
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30
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31 self.excludeFiles = excludeFiles
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32 self.excludeFileManager= excludefilemanager.ExcludeFileManager( )
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33
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34 self.primerManager = primermanager.PrimerManager( eprimerOptions )
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35
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36 self.crossValidate = crossValidate
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37
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38
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39 utils.logMessage( "UniqPrimerFinder::__init__()", "Initializing UniqPrimerFinder - complete" )
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40
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41 def writeOutputFile( self, primers, outputFileName, maxresults = 100 ):
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42 '''
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43 primers: a list of PrimerSet obs
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44 '''
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45 ##outputFileName = uPrimer ##Mau: defined this..
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46 outputFile = open( outputFileName, 'w' )
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47
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48 i = 0
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49 for primer in primers:
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50 i += 1
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51
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52 outputFile.write( "{0}\t{1}\t{2}\t{3}\n".format( i, primer.forwardPrimer, primer.reversePrimer, primer.productSize ) )
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53
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54 if i > maxresults:
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55 break
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56
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57 utils.logMessage( "UniqPrimerFinder::writeOutputFile()", "output file written." )
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58
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59
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60 def findPrimers( self, outputFile = "uPrimer.txt" ):
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61 outputFile = uPrimer ## Mau adds to overwrite the above value
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62
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63 utils.logMessage( "UniqPrimerFinder::findPrimers()", "Finding primers for include files" )
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64 startTime = time.time( )
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65 #generate the combined sequence fasta file for all exclude sequences
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66 utils.printProgressMessage( "*** Creating Combined Fasta File for Exclude Files ***" )
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67 for excludeFile in self.excludeFiles:
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68 self.excludeFileManager.addExcludeFile( excludeFile )
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69
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70 self.excludeFileManager.exportSequences( )
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71
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72 self.includeFileManager.setExcludeFile( self.excludeFileManager.getOutputFileName( ) )
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73
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74 utils.printProgressMessage( "*** Finding Sequences Unique to Target Genome ***" )
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75
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76 #run nucmer program on all include files
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77 for includeFile in self.includeFiles:
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78 self.includeFileManager.processIncludeFile( includeFile )
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79
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80 #get the sequences found in include files, but no the exclude file.
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81 uniqueSequences = self.includeFileManager.getUniqueSequences( )
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82
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83 utils.printProgressMessage( "*** Finding Primers ***" )
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84
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85 primers = self.primerManager.getPrimers( uniqueSequences )
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86
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87 if self.crossValidate == True:
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88 utils.printProgressMessage( "*** Cross Validating Primers ***" )
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89 primers = self.primerManager.crossValidatePrimers( primers, self.excludeFileManager.getOutputFileName( ) )
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90
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91
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92 utils.logMessage( "UniqPrimerFinder::findPrimers( )", "found {0} unique sequences".format( len( primers ) ) )
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93
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94 self.writeOutputFile( primers, outputFile )
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95
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96 utils.logMessage( "UniqPrimerFinder::findPrimers()", "Finished finding primers" )
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97 endTime = time.time()
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98 elapsedMinutes = int( ( endTime - startTime ) / 60 )
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99 elapsedSeconds = int( ( endTime - startTime ) % 60 )
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100 print "*** Time Elapsed: {0} minutes, {1} seconds ***".format( elapsedMinutes, elapsedSeconds )
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101 print "*** Output Written to {0} ***".format( outputFile )
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102
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103
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104 def printUsageAndQuit( ):
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105 global version
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106 print "uniqprimer - finds primers unique to a genome"
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107 print "Version: " + str( version )
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108 print "Summary of Options."
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109 print "Required Arguments:"
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110 print " -i <filename>: use <filename> as an include file. Primers will be identified for this genome"
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111 print " -x <filename>: use <filename> as an exclude file. Primers for this genome will be excluded"
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112 print " -o <filename>: specify the name of the unique primer output file (default is uPrimer.txt)" ## Mau added..
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113 print " -l <filename>: specify the name of the log output file" ## Mau added..
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114
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115 print "\nOptional Arguments:"
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116 print " --productsizerage: set a range for the desired size of PCR product (default=200-250). Example: ./uniqprimer -productsizerage 100-150"
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117 print " --primersize: set the desired primer size (default=20)"
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118 print " --minprimersize: set the minimum primer size (default=27)"
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119 print " --maxprimersize: set the maximum primer size (default=18)"
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120 print " --crossvalidate: force the program to cross validate primers against exclude files for extra certainty"
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121 print " --keeptempfiles: force the program to keep temporary files"
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122
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123 print "\n\nExample:"
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124 print "uniqprimer -i <includefile1> -i <includefile2> ... -i <includefileN> -x <excludefile1> -x <excludefile2> ... -x <excludefileN> -o primers.txt -l logfile.txt"
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125 utils.shutdownLogging( )
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126 sys.exit( )
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127
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128
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129 opts = 'i:x:h:o:l:' # Mau added :o & :l for outfile specification
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130 longopts=[ "productsizerange=", "primersize=", "minprimersize=", "maxprimersize=", "crossvalidate", "keeptempfiles" ]
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131
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132 def parseArgs( args ):
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133
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134
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135 global uPrimer ## Mau added lf, brute force...
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136 global lf # Mau added lf, brute force...
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137 #uPrimer = "uPrimer.txt" ##the default value...
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138
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139 crossValidate = False
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140 cleanup = True
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141 optlist, args = getopt.getopt( args, opts, longopts )
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142
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143 includeFiles = [ ]
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144 excludeFiles = [ ]
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145 eprimerOptions = utils.EPrimerOptions( )
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146
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147 verbose = False
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148 for opt in optlist:
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149 if opt[ 0 ] == '-i':
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150 includeFiles.append( opt[ 1 ] )
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151 elif opt[ 0 ] == '-x':
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152 excludeFiles.append( opt[ 1] )
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153 elif opt[ 0 ] == '-v':
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154 verbose = True
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155 elif opt[ 0 ] == '-o': ## Mau added, if -o...
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156 uPrimer = str(opt[1]) ## Mau added, then get filename for outfile after -o
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157 elif opt[ 0 ] == '-l': ## Mau added, if -l...
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158 lf = str(opt[1]) ## Mau added, then get filename for logfile after -l
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159 elif opt[ 0 ] == '--productsizerange':
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160 eprimerOptions.setProductRange( opt[ 1 ] )
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161 productsizerange = opt[ 1 ]
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162 elif opt[ 0 ] == '--primersize':
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163 eprimerOptions.setPrimerSize( opt[1 ] )
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164 elif opt[ 0 ] == '--minprimersize':
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165 eprimerOptions.setMinPrimerSize( opt[1 ] )
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166 elif opt[ 0 ] == '--maxprimersize':
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167 eprimerOptions.setMaxPrimerSize( opt[1 ] )
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168 elif opt[ 0 ] == '--crossvalidate':
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169 crossValidate = True
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170 elif opt[ 0 ] == '--crossvalidate':
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171 crossValidate = True
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172 elif opt[ 0 ] == '--keeptempfiles':
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173 cleanup = False
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174 elif opt[ 0 ] == '-h':
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175 printUsageAndQuit( )
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176 else:
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177 print "Unknown option: " + str( opt[ 0 ] )
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178 printUsageAndQuit( )
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179 #print "uPrimer: " + uPrimer + " log file name: " + lf + "\n"
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180 if len( includeFiles ) == 0 or len( excludeFiles ) == 0:
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181
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182 print "You must specify at least one include file and at least one exclude file"
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183 printUsageAndQuit( )
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184
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185 return includeFiles, excludeFiles, crossValidate, cleanup, verbose, eprimerOptions, lf , uPrimer #Mau: add lf, uPrime
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186
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187 def main( args, debug = False):
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188 #parse the command line arguments for include and exclude files
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189
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190 includeFiles, excludeFiles, crossValidate, cleanup, verbose, eprimerOptions, lf, uPrimer = parseArgs( args ) ##Mau add: lf
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191
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192 utils.initialize( True, cleanup, lf) ##Mau: add lf
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193
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194 #find primers for the include sequences
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195
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196 try:
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197 utils.logMessage( "uniqprimer::Main( )", "Logging include files: " )
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198 utils.logList( "uniqprimer::Main( )", includeFiles )
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199 utils.logMessage( "uniqprimer::Main( )", "Logging exclude files: " )
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200 utils.logList( "uniqprimer::Main( )", excludeFiles)
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201 print "*** Finding Primers ***"
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202 uniqPrimer = UniqPrimerFinder( includeFiles, excludeFiles, crossValidate, eprimerOptions)
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203 uniqPrimer.findPrimers( )
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204 except utils.NoFileFoundException as nfe:
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205 print "File not found: " + str( nfe.filename )
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206 printUsageAndQuit( )
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207 except utils.ProgramNotFoundException as pnfe:
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208 print str( pnfe.programName ) + ": program is not installed or is not in your path."
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209 print str( pnfe.details )
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210 except utils.NoPrimersExistException as npe:
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211 print "Failure: No unique primers exist for this combination"
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212 except exceptions.BaseException as e:
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213 print "It appears that an unknown sequence of events has resulted in the internal explosion of this program. Please send the file called \'log_uniqprimer.txt\' to herndon@cs.colostate.edu and tell that bonehead John to fix it!"
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214 print "Details:"
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215 print e
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216
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217 utils.shutdown( )
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218
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219 print "*** Finished ***"
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220
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221 if __name__ == '__main__':
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222
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223 #temp_args = "-i data/testdata/smallinclude.ffn -x data/testdata/smallexclude.ffn".split( )
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224
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225 #temp_args = "-i data/XOO_MAI1_scaffolds.fas -x data/KACC.ffn".split( )
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226 if len( sys.argv ) == 1:
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227 printUsageAndQuit( )
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228 main( sys.argv[ 1: ], debug = True )
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229
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