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 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