def test_single_protobuf_data():
filename = "test_data/test_single"
bd = jeweler_pb2.BraceletData()
bd.name = "TEST"
zleveldb.write_single_protobuf_data(filename, bd)
bd = jeweler_pb2.BraceletData()
zleveldb.load_single_protobuf_data(filename, bd)
assert("TEST" == bd.name)
def __init__(self, filename):
self.filename = filename
self.data = jeweler_pb2.CuffcompareData()
self.pseudo_set = pseudo.PseudoSet()
if False:
zleveldb.load_single_protobuf_data(self.protobuf_file, self.data)
else:
self.load_cuffcompare_raw_data(self.data)
zleveldb.write_single_protobuf_data(self.protobuf_file, self.data)
self.index = dict()
self.gene2num_exon = dict()
self.transcript2num_exon = dict()
self.build_index()
def load_mismatch_analyzer(self):
data = jeweler_pb2.TranscriptMismatcherAnalyzerData()
zleveldb.load_single_protobuf_data(self.shop_info.mismatch_analyzer_file, data)
ret = dict()
for d in data.location_result:
if d.coverage < 7:
continue
if d.num_mismatches < 5:
continue
if d.pvalue > 0 and math.log10(d.pvalue) > -19:
continue
if d.gene_id not in ret:
ret[d.gene_id] = set()
ret[d.gene_id].add(d.genome_location)
return ret