def __call__(self, track, slice = None ):
result = odict()
merged = None
rocs = []
for field in self.mFields:
data = []
for replicate in EXPERIMENTS.getTracks( track ):
statement = "SELECT contig, start, end,%(field)s FROM %(replicate)s_intervals" % locals()
data.append( self.get( statement) )
idx = []
for x in range(len(data)):
i = IndexedGenome.IndexedGenome()
for contig, start, end, peakval in data[x]:
i.add( contig, start, end, peakval )
idx.append( i )
def _iter( all ):
all.sort()
last_contig, first_start, last_end, last_value = all[0]
for contig, start, end, value in all[1:]:
if contig != last_contig or last_end < start:
yield (last_contig, first_start, last_end)
last_contig, first_start, last_end = contig, start, end
else:
last_end = max(last_end, end )
yield (last_contig, first_start, last_end)
if not merged:
all = [ x for x in itertools.chain( *data ) ]
merged = list( _iter(all) )
roc_data = []
for contig, start, end in merged:
intervals = []
for i in idx:
try:
intervals.append( list(i.get( contig, start, end )) )
except KeyError:
continue
if len(intervals) == 0:
continue
is_repro = len( [ x for x in intervals if x != [] ] ) == len(data)
value = max( [ x[2] for x in itertools.chain( *intervals )] )
# fpr, tpr
roc_data.append( (value, is_repro) )
roc_data.sort()
roc_data.reverse()
roc = zip(*Stats.computeROC( roc_data ))
result[field] = odict( (("FPR", roc[0]), (field,roc[1])) )
return result
def __call__(self, track, slice=None):
result = odict()
merged = None
rocs = []
for field in self.mFields:
data = []
for replicate in EXPERIMENTS.getTracks(track):
statement = "SELECT contig, start, end,%(field)s FROM %(replicate)s_intervals" % locals()
data.append(self.get(statement))
idx = []
for x in range(len(data)):
i = IndexedGenome.IndexedGenome()
for contig, start, end, peakval in data[x]:
i.add(contig, start, end, peakval)
idx.append(i)
def _iter(all):
all.sort()
last_contig, first_start, last_end, last_value = all[0]
for contig, start, end, value in all[1:]:
if contig != last_contig or last_end < start:
yield (last_contig, first_start, last_end)
last_contig, first_start, last_end = contig, start, end
else:
last_end = max(last_end, end)
yield (last_contig, first_start, last_end)
if not merged:
all = [x for x in itertools.chain(*data)]
merged = list(_iter(all))
roc_data = []
for contig, start, end in merged:
intervals = []
for i in idx:
try:
intervals.append(list(i.get(contig, start, end)))
except KeyError:
continue
if len(intervals) == 0:
continue
is_repro = len([x for x in intervals if x != []]) == len(data)
value = max([x[2] for x in itertools.chain(*intervals)])
# fpr, tpr
roc_data.append((value, is_repro))
roc_data.sort()
roc_data.reverse()
roc = zip(*Stats.computeROC(roc_data))
result[field] = odict((("FPR", roc[0]), (field, roc[1])))
return result
