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1 '''
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2 Created on Jan 1, 2011
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3
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4 @author: John L. Herndon
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5 @contact: herndon@cs.colostate.edu
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6 @organization: Colorado State University
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7 @group: Computer Science Department, Asa Ben-Hur's laboratory
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8 '''
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9
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10 import utils
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11 import tempfile
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12 import programs
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13 import eprimerparser
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14 import primersearchutils
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15 import fastaparser
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16 import exceptions
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17
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18
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19
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20
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21 class PrimerManager( object ):
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22 '''
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23 A class used to find primers given a set of sequences.
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24 '''
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25
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26 def __init__( self, eprimerOptions ):
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27 self.eprimer = programs.Eprimer( eprimerOptions )
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28 self.primersearch = programs.PrimerSearch( )
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29
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30
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31 def findPrimers( self, sequences, outputFile, primerpairs = 20, returnPrimers = False ):
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32 '''
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33 A method to find a set of primers based on the given sequences
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34 '''
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35
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36 utils.logMessage( "PrimerManager::findPrimer(s )", "writing sequences to a fasta file" )
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37
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38 #eleminate all sequences that are lees than the desired amplification size...
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39
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40 if len( sequences ) == 4 :
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41 print sequences
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42 sequences = filter( lambda x: len( x ) >= 200, sequences )
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43
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44 primerFastaFile = utils.getTemporaryDirectory( ) + "/sequenceForEprimer.fasta"
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45 fastaparser.writeFastaFile( sequences, primerFastaFile )
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46
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47 utils.logMessage( "PrimerManager::findPrimers( )", "executing eprimer3 program" )
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48 self.eprimer.execute( [ primerFastaFile, outputFile ] )
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49 utils.logMessage( "PrimerManager::findPrimer( )", "eprimer3 file {0} created. Parsing for primers.".format( outputFile ) )
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50
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51 primers = eprimerparser.parsePrimerSequences( outputFile )
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52
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53 utils.logMessage( "PrimerManager::findPrimers( )", "parsing for sequences complete" )
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54
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55 if returnPrimers == True:
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56 return primers
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57
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58
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59 def getPrimers( self, sequences ):
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60
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61 utils.logMessage( "PrimerManager::getCommonPrimers", "finding primers that are common to all include files" )
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62
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63 if len( sequences ) == 0:
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64 raise utils.NoPrimersExistException( )
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65
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66 referenceEPrimerFile = utils.getTemporaryDirectory( ) + "/referenceprimers.ep3"
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67
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68 #run eprimer to find primers in the reference file
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69 primers = self.findPrimers( sequences, referenceEPrimerFile, 20, True )
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70
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71
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72 if len( primers ) == 0:
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73 raise utils.NoPrimersExistException( )
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74
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75 return primers
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76
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77 def crossValidatePrimers2( self, primers, includeFile, j ):
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78 includeSequences = fastaparser.parseFastaFile( includeFile )
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79 #write a primer search input file with using the primers argument
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80 primerInputFileName = utils.getTemporaryDirectory( ) + "/tmpinputprimers2.ps" + str(j)
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81 primerOutputFileName = utils.getTemporaryDirectory( ) + "/tmpoutputprimers2.ps" + str(j)
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82 primersearchutils.writePrimerSearchInputFile( primers, primerInputFileName )
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83
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84 utils.logMessage( "PrimerManager::crossValidatePrimers", "finding primers that are in the supplied include file" )
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85 #run primer search to identify the primers
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86 self.primersearch.execute( [ includeFile, primerInputFileName, primerOutputFileName, "0" ] )
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87
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88 #read the found primers from the file
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89 commonPrimers = primersearchutils.parsePrimerSearchFile( primerOutputFileName )
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90
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91 #compose a list of primers that are not found in the exclude file...
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92 returnValue = [ ]
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93
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94 for primer in primers:
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95 if primer.id in commonPrimers:
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96 returnValue.append( primer )
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97
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98 utils.logMessage( "PrimerManager::crossValidatePrimers", "{0} unique primers identified out of {1}".format( len( returnValue ), len( primers ) ) )
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99
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100 if len( returnValue ) == 0:
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101 raise utils.NoPrimersExistException( )
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102
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103 return returnValue
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104
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105
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106 def crossValidatePrimers( self, primers, excludeFile ):
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107
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108 excludeSequences = fastaparser.parseFastaFile( excludeFile )
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109
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110 #write a primer search input file with using the primers argument
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111 primerInputFileName = utils.getTemporaryDirectory( ) + "/tmpinputprimers.ps"
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112 primerOutputFileName = utils.getTemporaryDirectory( ) + "/tmpoutputprimers.ps"
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113 primersearchutils.writePrimerSearchInputFile( primers, primerInputFileName )
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114
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115 utils.logMessage( "PrimerManager::crossValidatePrimers", "finding primers that are not in the supplied exclude file" )
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116 #run primer search to identify the primers
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1
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117 self.primersearch.execute( [ excludeFile, primerInputFileName, primerOutputFileName, "10" ] )
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0
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118
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119 #read the found primers from the file
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120 commonPrimers = primersearchutils.parsePrimerSearchFile( primerOutputFileName )
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121
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122 #compose a list of primers that are not found in the exclude file...
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123 returnValue = [ ]
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124
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125 for primer in primers:
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126 if primer.id not in commonPrimers:
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127 returnValue.append( primer )
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128
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129 utils.logMessage( "PrimerManager::crossValidatePrimers", "{0} unique primers identified out of {1}".format( len( returnValue ), len( primers ) ) )
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130
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131 if len( returnValue ) == 0:
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132 raise utils.NoPrimersExistException( )
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133
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134 return returnValue
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135
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136
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137
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