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1 import os
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2 from commons.pyRepetUnit.hmmer.hmmOutput.HmmOutput import HmmOutput
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3
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4 ##Concrete implementation for hmmscan and hmmpfam output methods
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5 #
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6 class HmmOutputProcessing (object):
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7
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8 ## write a align file from a HmmOutput object
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9 #
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10 # @param fout handle of align file
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11 # @param HmmOutput HmmOutput object in fact a list of hmmOutput containing datas required
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12 #
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13 def writeHmmOutputToAlignFile( self, pfamOutput, fout ):
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14 for item in pfamOutput.getList():
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15 for i in item:
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16 fout.write(i + "\t")
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17 fout.write("0\n")
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18
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19 ## read an output file from hmm profiles search program and write the corresponding .align file
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20 #
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21 # @param inputFile file
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22 # @param outputFile file
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23 #
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24 def readHmmOutputsAndWriteAlignFile( self, inputFile, outputFile ):
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25 if not os.path.exists(inputFile):
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26 print "Warning your input file " + inputFile + " does not exist!\n"
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27 return
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28 file2parse = open( inputFile )
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29 pfamOutput = HmmOutput()
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30 if outputFile == "":
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31 print "Warning have to specify an output name file!\n"
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32 return
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33 fout = open(outputFile, "w")
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34 while pfamOutput != None:
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35 pfamOutput = self.readHmmOutput(file2parse)
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36 if pfamOutput != None:
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37 self.writeHmmOutputToAlignFile(pfamOutput, fout)
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38 fout.close()
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39 file2parse.close()
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