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))
