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