uniqprimer: uniqprimer-0.5.0/primertools/primersearchutils.py comparison

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-:7e0438dad4e9
+:3249d78ecfc2
+'''
+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
+def writePrimerSearchInputFile( primerSets, outputFile ):
+'''
+A function to write primer pairs to a file formatted as primer search input.
+primerPairs - a list of utils.PrimerSet objects
+outputFile - a string containing the path to the output file
+'''
+file = open( outputFile, 'w' )
+i = 0
+for primerSet in primerSets:
+i += 1
+if primerSet.reversePrimer == "":
+print "Error - primer {0} has no reverse primer. {1} primers total".format( i, len( primerSets ) )
+continue
+file.write( primerSet.id + "\t" + primerSet.forwardPrimer + "\t" + primerSet.reversePrimer + "\n" )
+file.close( )
+def parsePrimerSearchFile( primerSearchFileName ):
+'''
+return a list of primer ids that are associated with at least one amplimer in the primer search output file.
+'''
+found = [ ]
+amplimerFound = False
+currentId = -1;
+for line in open( primerSearchFileName ).readlines( ):
+if "Primer name" in line:
+#the id of the primer is found after the string "Primer name" in the file
+currentId = line.split( ' ' )[ 2: ][ 0 ].strip( )
+elif "Amplimer" in line and currentId not in found:
+found.append( currentId )
+if amplimerFound == True:
+found.append( currentId )
+return found

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