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1 from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing
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2 ##data processor : read an output from hmmscan and transform it into .align file
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3 #
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4 class HmmscanOutput2align( object ):
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5
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6 ## constructor
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7 #
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8 def __init__(self):
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9 self.hmmscanOutputProcess = HmmscanOutputProcessing()
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10 self._inputFile = ""
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11 self._outputFile = ""
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12
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13 ## set input file
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14 #
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15 # @param input file input file
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16 #
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17 def setInputFile(self, input):
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18 self._inputFile = input
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19 ## set output file
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20 # @param output file output file
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21 #
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22 def setOutputFile(self, output):
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23 self._outputFile = output
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24
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25 ##read a hmmscan output file, parse it and, write the corresponding .align file
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26 #
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27 def run( self ):
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28 self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )
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