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comparison commons/pyRepetUnit/align/hmmOutputParsing/HmmscanOutput2align.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 from commons.pyRepetUnit.hmmer.hmmOutput.HmmscanOutputProcessing import HmmscanOutputProcessing
2 ##data processor : read an output from hmmscan and transform it into .align file
3 #
4 class HmmscanOutput2align( object ):
5
6 ## constructor
7 #
8 def __init__(self):
9 self.hmmscanOutputProcess = HmmscanOutputProcessing()
10 self._inputFile = ""
11 self._outputFile = ""
12
13 ## set input file
14 #
15 # @param input file input file
16 #
17 def setInputFile(self, input):
18 self._inputFile = input
19 ## set output file
20 # @param output file output file
21 #
22 def setOutputFile(self, output):
23 self._outputFile = output
24
25 ##read a hmmscan output file, parse it and, write the corresponding .align file
26 #
27 def run( self ):
28 self.hmmscanOutputProcess.readHmmOutputsAndWriteAlignFile( self._inputFile, self._outputFile )