--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniqprimer-0.5.0/build/lib/primertools/programs.py	Mon Jan 03 09:56:55 2022 +0000
@@ -0,0 +1,141 @@
+'''
+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 utils
+import os
+import subprocess
+
+
+class ProgramBase( object ):
+    
+    def __init__( self ):
+    
+        self.programName = None
+        self.proc = None
+    
+    def getProcessArgs( self, args ):
+        crash #abstract
+        
+    def execute( self, args, async = False ):
+        '''
+        run the nucmer program with a given compare file and an exclude file
+        '''
+        
+        utils.logMessage( "ProgramBase::Execute( )", "Running the {0} program.".format( self.programName ) )
+        
+        args, outputFile = self.getProcessArgs( args )
+        
+        print "*** Running {0} ***".format( self.programName )
+        
+        utils.logList( "ProgramBase::Execute( )", args )
+        
+        proc = subprocess.Popen( args )
+        
+        if async == False:
+            #wait for the nucmer instance to finish
+            proc.wait( )
+            print "*** Running {0} Complete ***".format( self.programName )
+        
+        #return the name of the coords file
+        return outputFile
+    
+    def isFinished( self ):
+        ifIsFinished 
+        
+class Nucmer( ProgramBase ):
+    
+    def __init__( self ):
+        #if we can't find the nucemer binary, throw
+        nucmerPath = utils.search_file( 'nucmer' )
+        ProgramBase.__init__( self )
+        if nucmerPath is None:
+            raise utils.ProgramNotFoundException( 'nucmer', "Please ensure that the MUMmer package is installed and configured on your system." )
+        
+        self.nucmer = nucmerPath
+
+        self.programName = "nucmer"
+        self.outputExtension = ".coords"
+        
+        
+    def getProcessArgs( self, inputArgs ):
+        
+        
+        time = utils.getTimeStamp( )
+        
+        identifier =  "nucmer_alignments"
+        args = [ self.nucmer, '-p', identifier, '-o', '--minmatch', '300', '--maxgap', '1' ]
+        
+        args.extend( inputArgs )
+    
+        outputFile = "{0}.coords".format( identifier )
+        
+        return args, outputFile
+
+class Eprimer( ProgramBase ):
+    
+    def __init__( self, eprimerOptions ):
+            
+        self.programName = "EPrimer3"
+        self.options = eprimerOptions
+        
+        primer3corePath = utils.search_file( "primer3_core" )
+        if primer3corePath is None:
+            raise utils.ProgramNotFoundException( "primer3_core", "Please ensure that the primer3 package is installed on your system. It can be obtained from http://primer3.sourceforge.net/" )
+        
+        eprimerPath = utils.search_file( "eprimer3" )
+        if eprimerPath is None:
+            raise utils.ProgramNotFoundException( 'eprimer3', "Please ensure that the EMBOSS package is installed and configured on your system." )
+        
+        self.primer3core = primer3corePath
+        self.eprimer3 = eprimerPath
+        
+    def getProcessArgs( self, inputArgs ):
+
+        #todo - allow user to determine output file location/name
+        
+        inputFasta = inputArgs[ 0 ]
+        outputFile = inputArgs[ 1 ]
+        args = [ self.eprimer3, inputFasta, outputFile, '-numreturn', '2', '-prange', self.options.getProductRange( ), '-osize', str( self.options.getPrimerSize( ) ),
+                '-minsize', str( self.options.getMinPrimerSize( ) ), '-maxsize', str( self.options.getMaxPrimerSize( ) )]
+        
+        return args, outputFile
+    
+class PrimerSearch( ProgramBase ):
+    def __init__( self ):    
+
+        self.programName = "PrimerSearch"
+        primerSearchPath = utils.search_file( "primersearch" )
+        if primerSearchPath is None:
+            raise utils.ProgramNotFoundException( "primersearch", "Please ensure that the EMBOSS package is installed on your system." )
+    
+        self.primerSearch = primerSearchPath
+        
+    def getProcessArgs( self, inputArgs ):
+        '''
+        usage for this program: inputArgs is an array length 4
+        inputArgs[0] = sequence file
+        inputArgs[1] = primer pairs file
+        inputArgs[2] = output file name
+        inputArgs[3] = percent mismatch
+        '''
+        
+        args = [ self.primerSearch ]
+        args.extend( [ '-seqall', inputArgs[ 0 ] ] ) 
+        args.extend( [ '-infile', inputArgs[ 1 ] ] )
+        args.extend( [ '-mismatchpercent', inputArgs[ 3 ] ] )
+        args.extend( [ '-outfile', inputArgs[ 2 ] ] ) 
+    
+    
+        return args, inputArgs[ 2 ]
+    
+    
+    
+    
+