def getAlignInstance(self): iAlign = Align() lAttributes = [] lAttributes.append( self.range_query.seqname ) lAttributes.append( self.range_query.start ) lAttributes.append( self.range_query.end ) lAttributes.append( self.range_subject.seqname ) lAttributes.append( self.range_subject.start ) lAttributes.append( self.range_subject.end ) lAttributes.append( self.e_value ) lAttributes.append( self.score ) lAttributes.append( self.identity ) iAlign.setFromTuple( lAttributes ) return iAlign
def retrieveInitialSequenceHeadersForAlignFile( self, dNew2Init ): inFileHandler = open( self._inFile, "r" ) outFileHandler = open( self._outFile, "w" ) a = Align() while True: line = inFileHandler.readline() if line == "": break a.setFromTuple( line.split("\t") ) nameToBeReplaced = a.range_query.seqname if dNew2Init.has_key( nameToBeReplaced ): a.range_query.seqname = dNew2Init[ nameToBeReplaced ] nameToBeReplaced = a.range_subject.seqname if dNew2Init.has_key( nameToBeReplaced ): a.range_subject.seqname = dNew2Init[ nameToBeReplaced ] a.write( outFileHandler ) inFileHandler.close() outFileHandler.close()
def setFromTuple(self, tuple): self.id = int(tuple[0]) Align.setFromTuple(self, tuple[1:])