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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 utils
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11
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12 def writePrimerSearchInputFile( primerSets, outputFile ):
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13 '''
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14 A function to write primer pairs to a file formatted as primer search input.
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15 primerPairs - a list of utils.PrimerSet objects
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16 outputFile - a string containing the path to the output file
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17 '''
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18
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19 file = open( outputFile, 'w' )
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20 i = 0
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21 for primerSet in primerSets:
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22 i += 1
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23 if primerSet.reversePrimer == "":
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24 print "Error - primer {0} has no reverse primer. {1} primers total".format( i, len( primerSets ) )
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25 continue
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26 file.write( primerSet.id + "\t" + primerSet.forwardPrimer + "\t" + primerSet.reversePrimer + "\n" )
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27
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28 file.close( )
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29
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30 def parsePrimerSearchFile( primerSearchFileName ):
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31 '''
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32 return a list of primer ids that are associated with at least one amplimer in the primer search output file.
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33 '''
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34 found = [ ]
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35
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36 amplimerFound = False
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37 currentId = -1;
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38 for line in open( primerSearchFileName ).readlines( ):
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39
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40 if "Primer name" in line:
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41 #the id of the primer is found after the string "Primer name" in the file
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42 currentId = line.split( ' ' )[ 2: ][ 0 ].strip( )
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43 elif "Amplimer" in line and currentId not in found:
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44 found.append( currentId )
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45
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46 if amplimerFound == True:
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47 found.append( currentId )
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48
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49 return found
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50
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51
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52
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53
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54
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55 |
