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:])
