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1 from commons.pyRepetUnit.hmmer.hmmOutput.HmmpfamOutputProcessing import HmmpfamOutputProcessing
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2
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3 ##data processor : read an output from hmmpfam and transform it into .align file
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4 #
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5 class HmmpfamOutput2align( object ):
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6
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7 ## constructor
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8 #
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9 def __init__(self):
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10 self.hmmpfamOutputProcess = HmmpfamOutputProcessing()
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11 self._inputFile = ""
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12 self._outputFile = ""
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13
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14 ## set input file
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15 #
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16 # @param input file input file
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17 #
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18 def setInputFile(self, input):
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19 self._inputFile = input
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20
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21 ## set output file
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22 #
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23 # @param output file output file
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24 #
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25 def setOutputFile(self, output):
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26 self._outputFile = output
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27
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28
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29 ##read a hmmpfam output file, parse it and, write the corresponding .align file
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30 #
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31 def run( self ):
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32 self.hmmpfamOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )
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