--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniqprimer-0.5.0/uniqprimer.py	Mon Jan 03 09:56:55 2022 +0000
@@ -0,0 +1,256 @@
+#!/usr/bin/python
+
+'''
+Created on Jan 1, 2011
+
+@author: John L. Herndon
+@contact: herndon@cs.colostate.edu
+@organization: Colorado State University
+@group: Computer Science Department, Asa Ben-Hur's laboratory 
+'''
+
+import exceptions
+import sys
+import time
+import os ## added by Alexis
+
+sys.path.append("/gs7k1/home/galaxy/galaxy_env/lib/python2.7/site-packages")
+
+import getopt
+from primertools import *
+
+version="0.5.0"
+
+
+class UniqPrimerFinder( object ):
+    
+    def __init__( self, includeFiles, excludeFiles, crossValidate, eprimerOptions):
+        
+        utils.logMessage( "UniqPrimerFinder::__init__()", "Initializing UniqPrimerFinder" )
+        self.includeFiles = includeFiles
+        self.includeFileManager = includefilemanager.IncludeFileManager( )
+        
+        self.excludeFiles = excludeFiles
+        self.excludeFileManager= excludefilemanager.ExcludeFileManager( )
+        
+        self.primerManager = primermanager.PrimerManager( eprimerOptions )
+        
+        self.crossValidate = crossValidate
+
+       
+        utils.logMessage( "UniqPrimerFinder::__init__()", "Initializing UniqPrimerFinder - complete" )
+    
+    def writeOutputFile( self, primers, outputFileName, maxresults = 100 ):
+        '''
+        primers: a list of PrimerSet obs
+        '''
+        ##outputFileName = uPrimer ##Mau: defined this..
+        outputFile = open( outputFileName, 'w' )
+        
+        i = 0
+        for primer in primers:
+            i += 1
+            
+            outputFile.write( "{0}\t{1}\t{2}\t{3}\n".format( i, primer.forwardPrimer, primer.reversePrimer, primer.productSize ) )
+            
+            if i > maxresults:
+                break
+            
+        utils.logMessage( "UniqPrimerFinder::writeOutputFile()", "output file written." )
+            
+    
+    def findPrimers( self, outputFile = "uPrimer.txt" ):
+	outputFile = uPrimer ## Mau adds to overwrite the above value
+	
+
+        utils.logMessage( "UniqPrimerFinder::findPrimers()", "Finding primers for include files" )
+        startTime = time.time( )
+        #generate the combined sequence fasta file for all exclude sequences
+        utils.printProgressMessage( "*** Creating Combined Fasta File for Exclude Files ***" )
+        for excludeFile in self.excludeFiles:
+            self.excludeFileManager.addExcludeFile( excludeFile )
+        
+        self.excludeFileManager.exportSequences( )
+        
+        self.includeFileManager.setExcludeFile( self.excludeFileManager.getOutputFileName( ) )
+
+        utils.printProgressMessage( "*** Finding Sequences Unique to Target Genome ***" )
+
+        #run nucmer program on all include files
+        for includeFile in self.includeFiles:
+            self.includeFileManager.processIncludeFile( includeFile )
+                
+        #get the sequences found in include files, but no the exclude file. 
+        uniqueSequences = self.includeFileManager.getUniqueSequences( )
+        
+        utils.printProgressMessage( "*** Finding Primers ***" )
+        
+        primers = self.primerManager.getPrimers( uniqueSequences )
+         
+        if self.crossValidate == True:
+            utils.printProgressMessage( "*** Cross Validating Primers ***" )
+            primers = self.primerManager.crossValidatePrimers( primers, self.excludeFileManager.getOutputFileName( ) )
+            # added by Alexis, primersearch also against all include files
+            #run primersearch program on all include files
+            j=0
+            for includeFile in self.includeFiles: # added by Alexis
+                j = j + 1
+                primers = self.primerManager.crossValidatePrimers2( primers, includeFile, j) # added by Alexis
+       		
+ 
+        utils.logMessage( "UniqPrimerFinder::findPrimers( )", "found {0} unique sequences".format( len( primers ) ) ) 
+        
+        self.writeOutputFile( primers, outputFile )
+        
+        utils.logMessage( "UniqPrimerFinder::findPrimers()", "Finished finding primers" )
+        endTime = time.time()
+        elapsedMinutes = int( ( endTime - startTime ) / 60 )
+        elapsedSeconds = int( ( endTime - startTime ) % 60 )
+        print "*** Time Elapsed: {0} minutes, {1} seconds ***".format( elapsedMinutes, elapsedSeconds )
+        print "*** Output Written to {0} ***".format( outputFile )
+        
+
+def printUsageAndQuit( ):
+    global version  
+    print "uniqprimer - finds primers unique to a genome"
+    print "Version: " + str( version )
+    print "Summary of Options."
+    print "Required Arguments:"
+    print " -i <filename>: use <filename> as an include file. Primers will be identified for this genome"
+    print " -x <filename>: use <filename> as an exclude file. Primers for this genome will be excluded"
+    print " -o <filename>: specify the name of the unique primer output file (default is uPrimer.txt)" ## Mau added..
+    print " -l <filename>: specify the name of the log output file" ## Mau added..
+    print " -f <filename>: specify the name of the Fasta of differential sequences" ## Alexis added..
+
+    print "\nOptional Arguments:"
+    print " --productsizerage: set a range for the desired size of PCR product (default=200-250). Example: ./uniqprimer -productsizerage 100-150"
+    print " --primersize: set the desired primer size (default=20)"
+    print " --minprimersize: set the minimum primer size (default=27)"
+    print " --maxprimersize: set the maximum primer size (default=18)"
+    print " --crossvalidate: force the program to cross validate primers against exclude files for extra certainty"
+    print " --keeptempfiles: force the program to keep temporary files"
+    
+    print "\n\nExample:"
+    print "uniqprimer -i <includefile1> -i <includefile2> ... -i <includefileN> -x <excludefile1> -x <excludefile2> ... -x <excludefileN> -o primers.txt -l logfile.txt -f seqForPrimer3.fa"
+    utils.shutdownLogging( )
+    sys.exit( )
+
+
+opts = 'i:x:h:o:l:f:' # Mau added :o & :l for outfile specification, Alexis added :f 
+longopts=[ "productsizerange=", "primersize=", "minprimersize=", "maxprimersize=", "crossvalidate", "keeptempfiles" ]
+
+def parseArgs( args ):
+
+
+    global uPrimer ## Mau added lf, brute force...
+    global lf # Mau added lf, brute force...
+    global fastaDiff # Alexis added fastaDiff
+    #uPrimer = "uPrimer.txt" ##the default value...
+
+    crossValidate = False
+    cleanup = True
+    optlist, args = getopt.getopt( args, opts, longopts )
+    
+    includeFiles = [ ]
+    excludeFiles = [ ]
+    eprimerOptions = utils.EPrimerOptions( )
+    
+    verbose = False
+    for opt in optlist:
+        if opt[ 0 ] == '-i':
+            includeFiles.append( opt[ 1 ] )
+        elif opt[ 0 ] == '-x':
+            excludeFiles.append( opt[ 1] )
+        elif opt[ 0 ] == '-v':
+            verbose = True 
+        elif opt[ 0 ] == '-o': ## Mau added, if -o...
+            uPrimer = str(opt[1])  ## Mau added, then get filename for outfile after -o
+        elif opt[ 0 ] == '-l': ## Mau added, if -l...
+            lf = str(opt[1])  ## Mau added, then get filename for logfile after -l
+        elif opt[ 0 ] == '-f': ## Alexis added, if -f
+            fastaDiff = str(opt[1]) ## Alexis added, then get filename for fasta file after -f
+        elif opt[ 0 ] == '--productsizerange':
+            eprimerOptions.setProductRange( opt[ 1 ] )
+            productsizerange = opt[ 1 ]
+        elif opt[ 0 ] == '--primersize':
+            eprimerOptions.setPrimerSize( opt[1 ] )
+        elif opt[ 0 ] == '--minprimersize':
+            eprimerOptions.setMinPrimerSize( opt[1 ] )
+        elif opt[ 0 ] == '--maxprimersize':
+            eprimerOptions.setMaxPrimerSize( opt[1 ] )
+        elif opt[ 0 ] == '--crossvalidate':
+            crossValidate = True
+        elif opt[ 0 ] == '--crossvalidate':
+            crossValidate = True
+        elif opt[ 0 ] == '--keeptempfiles':
+            cleanup = False
+        elif opt[ 0 ] == '-h':
+            printUsageAndQuit( )
+        else:
+            print "Unknown option: " + str( opt[ 0 ]  )
+            printUsageAndQuit( )
+    #print "uPrimer: " + uPrimer + " log file name: " + lf + "\n"
+    if len( includeFiles ) == 0 or len( excludeFiles ) == 0:
+        
+        print "You must specify at least one include file and at least one exclude file"
+        printUsageAndQuit( )
+
+    return includeFiles, excludeFiles, crossValidate, cleanup, verbose, eprimerOptions, lf , uPrimer, fastaDiff  #Mau: add lf, uPrime
+
+def main( args, debug = False):
+    #parse the command line arguments for include and exclude files
+    
+    includeFiles, excludeFiles, crossValidate, cleanup, verbose, eprimerOptions, lf, uPrimer, fastaDiff = parseArgs( args ) ##Mau add: lf
+    utils.initialize( True, cleanup, lf)  ##Mau: add lf
+    #find primers for the include sequences
+   
+    tmpdir = utils.getTemporaryDirectory() ## added by Alexis
+    command = "cp -rf " + tmpdir + "/sequenceForEprimer.fasta" + " " + fastaDiff
+ 
+    try:
+        utils.logMessage( "uniqprimer::Main( )", "Logging include files: " )
+        utils.logList( "uniqprimer::Main( )", includeFiles )
+        utils.logMessage( "uniqprimer::Main( )", "Logging exclude files: " ) 
+        utils.logList( "uniqprimer::Main( )", excludeFiles)
+        print "*** Finding Primers ***"
+        uniqPrimer = UniqPrimerFinder( includeFiles, excludeFiles, crossValidate, eprimerOptions) 
+        uniqPrimer.findPrimers( )
+    except utils.NoFileFoundException as nfe:
+        print "File not found: " + str( nfe.filename )
+        printUsageAndQuit( )
+    except utils.ProgramNotFoundException as pnfe:
+        print str( pnfe.programName ) + ": program is not installed or is not in your path."
+        print str( pnfe.details )
+    except utils.NoPrimersExistException as npe:
+        print "Failure: No unique primers exist for this combination"
+    except exceptions.BaseException as e:
+        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!"
+        print "Details:"
+        print e    
+    
+    os.system("cp -rf " + tmpdir + "/sequenceForEprimer.fasta" + " " + fastaDiff)
+    utils.shutdown( )
+
+    print "*** Finished ***"
+    
+if __name__ == '__main__':
+    
+    #temp_args = "-i data/testdata/smallinclude.ffn -x data/testdata/smallexclude.ffn".split( )
+    
+    #temp_args = "-i data/XOO_MAI1_scaffolds.fas -x data/KACC.ffn".split( )
+    if len( sys.argv ) == 1:
+        printUsageAndQuit( )
+    main( sys.argv[ 1: ], debug = True )
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+