def convertPathFileIntoMapFileWithQueryCoordsOnly( pathFile, mapFile ):
pathFileHandler = open( pathFile, "r" )
mapFileHandler = open( mapFile, "w" )
p = Path()
while True:
line = pathFileHandler.readline()
if line == "":
break
p.reset()
p.setFromTuple( line.split("\t") )
p.writeSubjectAsMapOfQuery( mapFileHandler )
pathFileHandler.close()
mapFileHandler.close()
def getPathInstance( self ):
p = Path()
tuple = ( self.id,
self.range_query.seqname,
self.range_query.start,
self.range_query.end,
self.range_subject.seqname,
self.range_subject.start,
self.range_subject.end,
self.e_value,
self.score,
self.identity )
p.setFromTuple( tuple )
return p
def retrieveInitialSequenceHeadersForPathFile( self, dNew2Init ):
inFileHandler = open( self._inFile, "r" )
outFileHandler = open( self._outFile, "w" )
p = Path()
while True:
line = inFileHandler.readline()
if line == "":
break
p.setFromTuple( line.split("\t") )
nameToBeReplaced = p.range_query.seqname
if dNew2Init.has_key( nameToBeReplaced ):
p.range_query.seqname = dNew2Init[ nameToBeReplaced ]
nameToBeReplaced = p.range_subject.seqname
if dNew2Init.has_key( nameToBeReplaced ):
p.range_subject.seqname = dNew2Init[ nameToBeReplaced ]
p.write( outFileHandler )
inFileHandler.close()
outFileHandler.close()
