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1 '''
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2 Created on Jan 1, 2011
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3
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4 @author: John L. Herndon
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5 @contact: herndon@cs.colostate.edu
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6 @organization: Colorado State University
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7 @group: Computer Science Department, Asa Ben-Hur's laboratory
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8 '''
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9
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10 import os
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11 import utils
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12 import re
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13
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14 def parsePrimerSequences( eprimerFile ):
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15 '''
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16 parse an eprimer3 output file for all primers
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17 '''
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18
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19 utils.logMessage( "eprimerparser::parsePrimerSequences( )", "parsing for primer sequences" )
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20 if os.path.exists( eprimerFile ) == False:
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21 utils.logMessage( "eprimerparser::parsePrimerSequences( )", "ERROR - eprimer file was not found" )
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22 raise utils.NoFileFoundException( eprimerFile )
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23
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24
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25 primers = [ ]
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26 primerFile = open( eprimerFile )
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27
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28 currentPrimer = None
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29
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30 nextPrimerId = 0
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31 for line in primerFile.readlines( ):
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32
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33 if line[ 0 ] == '# ':
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34 continue
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35
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36 if line.find( "PRODUCT SIZE" ) != -1:
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37 if currentPrimer is not None:
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38 primers.append( currentPrimer )
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39 currentPrimer = utils.PrimerSet( str( nextPrimerId ) )
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40 nextPrimerId += 1
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41 productSize = int( line.split( ':' )[ 1 ].strip( ) )
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42 currentPrimer.setProductSize( productSize )
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43 else:
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44 tokens = re.split( ' *', line.strip( ) )
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45 if len( tokens ) == 7:
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46
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47 sequence = tokens[ 6 ]
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48 temp = tokens[ 4 ]
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49
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50 if tokens[ 0 ] == "FORWARD":
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51 currentPrimer.setForwardPrimerData( sequence, temp )
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52 elif tokens[ 0 ] == "REVERSE":
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53 currentPrimer.setReversePrimerData( sequence, temp )
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54
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55 if currentPrimer is not None:
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56 primers.append( currentPrimer )
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57
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58 utils.logMessage( "eprimerparser::parsePrimerSequences( )", "finished parsing. found {0} primers".format( len( primers ) ) )
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59 return primers
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