--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniqprimer-0.5.0/primertools/eprimerparser.py	Mon Jan 03 09:56:55 2022 +0000
@@ -0,0 +1,75 @@
+'''
+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 os
+import utils
+import re
+
+def parsePrimerSequences( eprimerFile ):
+    '''
+    parse an eprimer3 output file for all primers
+    '''
+    
+    utils.logMessage( "eprimerparser::parsePrimerSequences( )", "parsing for primer sequences" )
+    if os.path.exists( eprimerFile ) == False:
+        utils.logMessage( "eprimerparser::parsePrimerSequences( )", "ERROR - eprimer file was not found" )
+        raise utils.NoFileFoundException( eprimerFile )
+    
+    
+    primers = [ ]
+    primerFile = open( eprimerFile )
+    
+    currentPrimer = None
+            
+    nextPrimerId = 0
+    for line in primerFile.readlines( ):
+        
+        if line[ 0 ] == '# ':
+            continue
+        
+        if line.find( "PRODUCT SIZE" ) != -1:
+            if currentPrimer is not None:
+                primers.append( currentPrimer )
+            currentPrimer = utils.PrimerSet( str( nextPrimerId ) )
+            nextPrimerId += 1
+            productSize = int( line.split( ':' )[ 1 ].strip( ) )
+            currentPrimer.setProductSize( productSize )
+        else:
+            tokens = re.split( ' *', line.strip( ) ) 
+            if len( tokens ) == 7:
+                
+                sequence = tokens[ 6 ]
+                temp = tokens[ 4 ]
+            
+                if tokens[ 0 ] == "FORWARD": 
+                    currentPrimer.setForwardPrimerData( sequence, temp )
+                elif tokens[ 0 ] == "REVERSE":
+                    currentPrimer.setReversePrimerData( sequence, temp )
+    
+    if currentPrimer is not None:
+        primers.append( currentPrimer )
+    
+    utils.logMessage( "eprimerparser::parsePrimerSequences( )", "finished parsing. found {0} primers".format( len( primers ) ) )
+    return primers        
+                
+            
+        
+        
+        
+        
+        
+        
+        
+        
+        
+        
+    
+    
+     
+    
\ No newline at end of file