def getSlice(self, seqID, start, stop):
'perform an interval query and return results as raw ivals'
try:
seq = self.seqDict[seqID]
nlmsa_id, ns, offset = self.seqs[seq] # GET UNION INFO FOR THIS SEQ
except KeyError:
return '' # failure code
ival = sequence.absoluteSlice(seq, start, stop) # GET THE INTERVAL
try:
myslice = self[ival] # DO THE QUERY
except EmptySliceError:
return 'EMPTY'
except KeyError:
return '' # FAILURE CODE
ivals = myslice.rawIvals() # GET RAW INTERVAL DATA
d = {}
# Save index info for source seq.
d[nlmsa_id] = self.seqs.IDdict[str(nlmsa_id)]
for v in ivals: # SAVE INDEX INFO FOR TARGET SEQS
id = v[2] # target_id NLMSA_ID
if not self.seqlist.is_lpo(id):
# Only non-LPO seqs stored in this index.
d[id] = self.seqs.IDdict[str(id)]
# XMLRPC can't handle int dictionaries, use a list.
l = [(key, val) for key, val in d.items()]
# List of aligned ivals, list of (nlmsa_id, (seqID, nsID)).
return nlmsa_id, ivals, l
def getSlice(self, seqID, start, stop):
"perform an interval query and return results as raw ivals"
try:
seq = self.seqDict[seqID]
nlmsa_id, ns, offset = self.seqs[seq] # GET UNION INFO FOR THIS SEQ
except KeyError:
return "" # failure code
ival = sequence.absoluteSlice(seq, start, stop) # GET THE INTERVAL
try:
myslice = self[ival] # DO THE QUERY
except EmptySliceError:
return "EMPTY"
except KeyError:
return "" # FAILURE CODE
ivals = myslice.rawIvals() # GET RAW INTERVAL DATA
d = {}
d[nlmsa_id] = self.seqs.IDdict[str(nlmsa_id)] # SAVE INDEX INFO FOR SOURCE SEQ
for v in ivals: # SAVE INDEX INFO FOR TARGET SEQS
id = v[2] # target_id NLMSA_ID
if not self.seqlist.is_lpo(id): # ONLY NON-LPO SEQS STORED IN THIS INDEX
d[id] = self.seqs.IDdict[str(id)]
l = [(key, val) for key, val in d.items()] # XMLRPC CAN'T HANDLE int DICT, SO USE LIST
return nlmsa_id, ivals, l # LIST OF ALIGNED IVALS, LIST OF (nlmsa_id,(seqID,nsID))
