def getMapInstance( self ):
iMap = Map()
lAttributes = []
lAttributes.append( self.name )
lAttributes.append( self.seqname )
lAttributes.append( self.start )
lAttributes.append( self.end )
iMap.setFromTuple( lAttributes )
return iMap
def getDictPerSeqNameFromMapFile( mapFile ):
dSeqName2Maps = {}
mapFileHandler = open( mapFile, "r" )
while True:
line = mapFileHandler.readline()
if line == "":
break
iMap = Map()
iMap.setFromString( line, "\t" )
if not dSeqName2Maps.has_key( iMap.seqname ):
dSeqName2Maps[ iMap.seqname ] = []
dSeqName2Maps[ iMap.seqname ].append( iMap )
mapFileHandler.close()
return dSeqName2Maps
def createAndLoadTable(self):
"""
Create the table and load the map data from input table
"""
self.db.create_table(self.db, self.tableName, "", "map")
f = open(self.inputFileName, "r")
iMap = Map()
lMap = []
while iMap.read(f):
lMap.append(iMap)
iMap = Map()
f.close()
self._tMapA = TableMapAdaptator(self.db, self.tableName)
self._tMapA.insMapList(lMap)
def mergeMatchesOnQueries(inFile, outFile):
mapFile = "%s.map" % ( inFile )
PathUtils.convertPathFileIntoMapFileWithQueryCoordsOnly( inFile, mapFile )
cmd = "mapOp"
cmd += " -q %s" % ( mapFile )
cmd += " -m"
cmd += " 2>&1 > /dev/null"
exitStatus = os.system( cmd )
if exitStatus != 0:
print "ERROR: mapOp returned %i" % ( exitStatus )
sys.exit(1)
os.remove( mapFile )
mergeFile = "%s.merge" % ( mapFile )
mergeFileHandler = open( mergeFile, "r" )
outFileHandler = open( outFile, "w" )
m = Map()
while True:
line = mergeFileHandler.readline()
if line == "":
break
m.reset()
m.setFromString( line, "\t" )
m.writeAsQueryOfPath( outFileHandler )
mergeFileHandler.close()
os.remove( mergeFile )
outFileHandler.close()
def getDictPerNameFromMapFile( mapFile ):
dName2Maps = {}
mapFileHandler = open( mapFile, "r" )
while True:
line = mapFileHandler.readline()
if line == "":
break
iMap = Map()
iMap.setFromString( line, "\t" )
if dName2Maps.has_key( iMap.name ):
if iMap == dName2Maps[ iMap.name ]:
continue
else:
msg = "ERROR: in file '%s' two different Map instances have the same name '%s'" % ( mapFile, iMap.name )
sys.stderr.write( "%s\n" % ( msg ) )
sys.exit(1)
dName2Maps[ iMap.name ] = iMap
mapFileHandler.close()
return dName2Maps
def diff(self, o):
iMap = Map.diff(self, o.getMap())
new = Set()
if not iMap.isEmpty():
new.id = self.id
new.name = self.name
new.seqname = self.seqname
new.start = iMap.start
new.end = iMap.end
return new
def getSubjectAsMapOfQuery(self):
iMap = Map()
iMap.name = self.range_subject.seqname
iMap.seqname = self.range_query.seqname
if self.range_subject.isOnDirectStrand():
iMap.start = self.range_query.start
iMap.end = self.range_query.end
else:
iMap.start = self.range_query.end
iMap.end = self.range_query.start
return iMap
def convertMapFileIntoSetFile( mapFileName, setFileName = "" ):
if setFileName == "":
setFileName = "%s.set" % mapFileName
mapFileHandler = open( mapFileName, "r" )
setFileHandler = open( setFileName, "w" )
iMap = Map()
count = 0
while True:
line = mapFileHandler.readline()
if line == "":
break
iMap.setFromString(line)
count += 1
iSet = Set()
iSet.id = count
iSet.name = iMap.getName()
iSet.seqname = iMap.getSeqname()
iSet.start = iMap.getStart()
iSet.end = iMap.getEnd()
iSet.write(setFileHandler)
mapFileHandler.close()
setFileHandler.close()
def merge(self, o):
if self.seqname == o.seqname:
Map.merge(self, o)
self.id = min(self.id, o.id)
def toString(self):
string = "%i" % (self.id)
string += "\t%s" % (Map.toString(self))
return string
def setFromTuple(self, tuple):
self.id = int(tuple[0])
Map.setFromTuple(self, tuple[1:])
def __eq__(self, o):
if self.id != o.id:
return False
else:
return Map.__eq__(self, o)
def __init__(self, id=-1, name="", seqname="", start=-1, end=-1):
Map.__init__( self, name, seqname, start, end )
self.id = id
def removeRedundantMembersDueToChunkOverlaps( dGroupId2MemberHeaders, dGr2Mb, chunkOverlap ):
# for each group
for groupID in dGroupId2MemberHeaders.keys():
if verbose > 1:
print "group %s:" % ( groupID )
if groupID not in [ "3446" ]:
#continue
pass
# get members into Map object, per chunk name
dChunkName2Map = {}
for memberH in dGroupId2MemberHeaders[ groupID ]:
if verbose > 1: print memberH
tokens = memberH.split(" ")
if "," not in tokens[3]:
m = Map()
m.name = tokens[0]
m.seqname = tokens[1]
m.start = int( tokens[3].split("..")[0] )
m.end = int( tokens[3].split("..")[1] )
dChunkName2Map[ m.seqname ] = [ m ]
else:
dChunkName2Map[ tokens[1] ] = []
for i in tokens[3].split(","):
m = Map()
m.name = tokens[0]
m.seqname = tokens[1]
m.start = int( i.split("..")[0] )
m.end = int( i.split("..")[1] )
dChunkName2Map[ m.seqname ].append( m )
# remove chunks without previous or next chunks
for chunkName in dChunkName2Map.keys():
chunkId = int( chunkName.split("chunk")[1] )
if not ( dChunkName2Map.has_key( "chunk%i" % ( chunkId + 1 ) ) \
or dChunkName2Map.has_key( "chunk%i" % ( chunkId - 1 ) ) ):
del dChunkName2Map[ chunkName ]
continue
# for each pair of chunk overlap, remove one chunk
lChunkNames = dChunkName2Map.keys()
lChunkNames.sort()
out = []
for i in range(0,len(lChunkNames), 2):
del dChunkName2Map[ lChunkNames[i] ]
# remove members outside chunk overlap (~< 10000 bp)
for chunkName in dChunkName2Map.keys():
out = []
for index, m in enumerate( dChunkName2Map[ chunkName ][:] ):
if m.getMax() <= 1.1 * chunkOverlap:
out.append( dChunkName2Map[ chunkName ][ index ] )
dChunkName2Map[ chunkName ] = out
if len(dChunkName2Map[ chunkName ]) == 0:
del dChunkName2Map[ chunkName ]
if verbose > 1:
print "all members:", dGr2Mb[ groupID ]
print "chunks to clean:", dChunkName2Map.keys()
lMembersToRemove = []
for i in dChunkName2Map.keys():
for j in dChunkName2Map[ i ]:
mbId = j.name.split("Gr")[0]
if "Q" in mbId:
mbId = mbId.split("Q")[1]
elif "S" in mbId:
mbId = mbId.split("S")[1]
lMembersToRemove.append( mbId )
out = []
for index, k in enumerate( dGr2Mb[ groupID ][:] ):
if k not in lMembersToRemove:
out.append( dGr2Mb[ groupID ][index] )
dGr2Mb[ groupID ] = out
if verbose > 1:
print "members to keep:", dGr2Mb[ groupID ]
sys.stdout.flush()
return dGr2Mb