def crossValidatePrimers( self, primers, excludeFile ):
excludeSequences = fastaparser.parseFastaFile( excludeFile )
#write a primer search input file with using the primers argument
primerInputFileName = utils.getTemporaryDirectory( ) + "/tmpinputprimers.ps"
primerOutputFileName = utils.getTemporaryDirectory( ) + "/tmpoutputprimers.ps"
primersearchutils.writePrimerSearchInputFile( primers, primerInputFileName )
utils.logMessage( "PrimerManager::crossValidatePrimers", "finding primers that are not in the supplied exclude file" )
#run primer search to identify the primers
self.primersearch.execute( [ excludeFile, primerInputFileName, primerOutputFileName, "0" ] )
#read the found primers from the file
commonPrimers = primersearchutils.parsePrimerSearchFile( primerOutputFileName )
#compose a list of primers that are not found in the exclude file...
returnValue = [ ]
for primer in primers:
if primer.id not in commonPrimers:
returnValue.append( primer )
utils.logMessage( "PrimerManager::crossValidatePrimers", "{0} unique primers identified out of {1}".format( len( returnValue ), len( primers ) ) )
if len( returnValue ) == 0:
raise utils.NoPrimersExistException( )
return returnValue
def processIncludeFile( self, includeFileName ):
"""
A function that adds and processes and include file.
An exclude file must be set for this function to be called.
"""
utils.logMessage( "IncludeFileManager::processIncludeFile( )", "processing {0}".format( includeFileName ) )
if self.isExcludeFileInitialized == False:
utils.logMessage( "IncludeFileManager::processIncludeFile( )", "no exclude file set".format( includeFileName ) )
raise utils.ModuleNotInitializedException( "includefilemanager", "no exclude file set" )
if self.isReferenceFileInitialized == False:
utils.logMessage( "IncludeFileManager::processIncludeFile( )", "running nucmer for reference file: {0}".format( includeFileName ) )
self.uniqueSequences = self.findUniqueSequencesInFile( includeFileName, self.excludeFileName )
self.referenceFile = includeFileName
self.isReferenceFileInitialized = True
else:
#write the unique sequences to a temp file
tempSequences = utils.getTemporaryDirectory( ) + "/tempSequences.fasta"
fastaparser.writeFastaFile( self.uniqueSequences, tempSequences )
self.findCommonSequencesInFile( includeFileName, tempSequences )
self.includeFiles.append( includeFileName )
def findPrimers( self, sequences, outputFile, primerpairs = 20, returnPrimers = False ):
'''
A method to find a set of primers based on the given sequences
'''
utils.logMessage( "PrimerManager::findPrimer(s )", "writing sequences to a fasta file" )
#eleminate all sequences that are lees than the desired amplification size...
if len( sequences ) == 4 :
print sequences
sequences = filter( lambda x: len( x ) >= 200, sequences )
primerFastaFile = utils.getTemporaryDirectory( ) + "/sequenceForEprimer.fasta"
fastaparser.writeFastaFile( sequences, primerFastaFile )
utils.logMessage( "PrimerManager::findPrimers( )", "executing eprimer3 program" )
self.eprimer.execute( [ primerFastaFile, outputFile ] )
utils.logMessage( "PrimerManager::findPrimer( )", "eprimer3 file {0} created. Parsing for primers.".format( outputFile ) )
primers = eprimerparser.parsePrimerSequences( outputFile )
utils.logMessage( "PrimerManager::findPrimers( )", "parsing for sequences complete" )
if returnPrimers == True:
return primers
def buildOutputFileName(self):
"""
build a unique file name to store the combined output sequences to
"""
self.outputFile = utils.getTemporaryDirectory(
) + "/combined_exlude.ffn"
utils.logMessage("ExcludeFileManager::buildOutputFileName( )",
" exclude file: {0}".format(self.outputFile))
def getPrimers( self, sequences ):
utils.logMessage( "PrimerManager::getCommonPrimers", "finding primers that are common to all include files" )
if len( sequences ) == 0:
raise utils.NoPrimersExistException( )
referenceEPrimerFile = utils.getTemporaryDirectory( ) + "/referenceprimers.ep3"
#run eprimer to find primers in the reference file
primers = self.findPrimers( sequences, referenceEPrimerFile, 20, True )
if len( primers ) == 0:
raise utils.NoPrimersExistException( )
return primers