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