def load_sequences(genome): name = genome + '_seq' print name if check_NamedIndividual(name): print name + " already in Blazegraph." else: try: try: (sequence, bp, contigs) = from_nuccore(genome) except ValueError: (sequence, bp, contigs) = from_ftp(genome) g = Graph() Sequence(g, name, genome, sequence, bp, contigs).rdf() upload_data(generate_output(g)) except TypeError: f = open(os.path.join(os.path.dirname(inspect.getfile(inspect.currentframe())), "outputs/seq_errors.txt"), "a") f.write(genome + ': The records for this sequence are not retrievable.\n') print "%s: The records for this sequence are not retrievable." %genome
def load_sequences(genome): name = genome + '_seq' print name if check_NamedIndividual(name): print name + " already in Blazegraph." else: try: try: (sequence, bp, contigs) = from_nuccore(genome) except ValueError: (sequence, bp, contigs) = from_ftp(genome) g = Graph() Sequence(g, name, genome, sequence, bp, contigs).rdf() upload_data(generate_output(g)) except TypeError: f = open( os.path.join( os.path.dirname(inspect.getfile(inspect.currentframe())), "outputs/seq_errors.txt"), "a") f.write(genome + ': The records for this sequence are not retrievable.\n') print "%s: The records for this sequence are not retrievable." % genome
def create_pending_genome(self): g = Graph() n = self.dict["name"] kwargs = {} if check_NamedIndividual(n): print n + " already in Blazegraph." else: self.add_ids(kwargs, n) for key, value in self.dict.iteritems(): if key in self.genome_params: param = self.genome_params.get(key) kwargs.update({param: value}) elif key == "serotype": (Otype, Htype) = self.return_serotypes(value) kwargs.update({"Otype": Otype, "Htype": Htype}) else: pass PendingGenome(g, **kwargs).rdf() ontology_uploader.upload_data(generate_output(g))
def create_pending_genome(self): g = Graph() n = self.dict["name"] kwargs = {} if check_NamedIndividual(n): print n + " already in Blazegraph." else: self.add_ids(kwargs, n) for key, value in self.dict.iteritems(): if key in self.genome_params: param = self.genome_params.get(key) kwargs.update({param:value}) elif key == "serotype": (Otype, Htype) = self.return_serotypes(value) kwargs.update({"Otype":Otype, "Htype":Htype}) else: pass PendingGenome(g, **kwargs).rdf() ontology_uploader.upload_data(generate_output(g))