def reset( self ):
Path.reset( self )
self.query_length = -1
self.query_length_perc = -1
self.query_seqlength = -1
self.match_length_perc = -1
self.subject_length = -1
self.subject_length_perc = -1
self.subject_seqlength = -1
def __init__(self):
Path.__init__(self)
self.query_length = -1
self.query_length_perc = -1 # length of the match on the query / length of the query
self.query_seqlength = -1
self.match_length_perc = -1 # length of the match on the query / total length of the subject
self.subject_length = -1
self.subject_length_perc = -1 # length of the match on the subject / length of the subject
self.subject_seqlength = -1
def getPathListFromFile( pathFile ):
lPaths = []
pathFileHandler = open( pathFile, "r" )
while True:
line = pathFileHandler.readline()
if line == "":
break
iPath = Path()
iPath.setFromString( line )
lPaths.append( iPath )
pathFileHandler.close()
return lPaths
def convertPathFileIntoSetFile( pathFile, setFile ):
pathFileHandler = open( pathFile, "r" )
setFileHandler = open( setFile, "w" )
iPath = Path()
while True:
line = pathFileHandler.readline()
if line == "":
break
iPath.setFromString( line )
iSet = iPath.getSubjectAsSetOfQuery()
iSet.write( setFileHandler )
pathFileHandler.close()
setFileHandler.close()
def convertPathFileIntoAlignFile(pathFile, alignFile):
pathFileHandler = open( pathFile, "r" )
alignFileHandler = open( alignFile, "w" )
iPath = Path()
while True:
line = pathFileHandler.readline()
if line == "":
break
iPath.setFromString( line )
iAlign = iPath.getAlignInstance()
iAlign.write( alignFileHandler )
pathFileHandler.close()
alignFileHandler.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 getDictOfListsWithIdAsKeyFromFile( pathFile ):
dId2PathList = {}
pathFileHandler = open( pathFile, "r" )
while True:
line = pathFileHandler.readline()
if line == "":
break
iPath = Path()
iPath.setFromString( line )
if dId2PathList.has_key( iPath.id ):
dId2PathList[ iPath.id ].append( iPath )
else:
dId2PathList[ iPath.id ] = [ iPath ]
pathFileHandler.close()
return dId2PathList
def __eq__(self, o):
if self.query_length != o.query_length or self.query_length_perc != o.query_length_perc\
or self.query_seqlength != o.query_seqlength or self.subject_length != o.subject_length\
or self.subject_length_perc != o.subject_length_perc or self.subject_seqlength != o.subject_seqlength\
or self.match_length_perc != o.match_length_perc:
return False
else:
return Path.__eq__(self, o)
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()
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()