--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniqprimer-0.5.0/primertools/excludefilemanager.py	Mon Jan 03 09:56:55 2022 +0000
@@ -0,0 +1,75 @@
+'''
+Created on Jan 16, 2011
+
+@author: jlh
+'''
+import utils
+import fastaparser
+from Bio import SeqIO
+import os
+
+class ExcludeFileManager( object ):
+    '''
+    A class to manage fasta files to be excluded
+    '''
+
+    def __init__( self ):
+        """
+        Initialize the ExcludeFileManager
+        """
+        self.excludeFiles = [ ]
+        self.outputFile = ""
+    
+    def getOutputFileName( self ):
+        """
+         get the name of the file combined-sequence fasta file
+        """
+        return self.outputFile
+    
+    def addExcludeFile( self,  excludeFile ):
+        """
+        add a file to be managed by the ExcludeFileManager
+        """
+        
+        if os.path.exists( excludeFile ) == False:
+            utils.logMessage( "ExcludeFileManager::addExcludeFile( )", "exclude file not found: {0}".format( excludeFile ) )
+            raise utils.NoFileFoundException( excludeFile )
+        
+        utils.logMessage( "ExcludeFileManager::addExcludeFile( )", "adding exclude file {0}".format( excludeFile ) )
+        self.excludeFiles.append( excludeFile )
+    
+    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 exportSequences( self ):
+        """
+        combine all exclude files into a single exclude file
+        """
+        
+        utils.logMessage( "ExcludeFileManager::exportSequences( )", "parsing exclude sequences")
+        
+        #read all exclude file sequences into memory
+        sequences = [ ]
+        for excludeFile in self.excludeFiles:
+            sequences.extend( fastaparser.parseFastaFile( excludeFile ) )
+        
+        utils.logMessage( "ExcludeFileManager::exportSequences( )", "finished parsing, writing to a common file"  )
+        
+        self.buildOutputFileName( )
+        #combine the sequences and write them to a file
+        
+        SeqIO.write( sequences, open( self.outputFile, "w" ), "fasta" )
+         
+        utils.logMessage( "ExcludeFileManager::exportSequences( )", "All sequences exported" )
+        
+        
+        
+        
+        
+    
+    
+        
\ No newline at end of file