def upload_missing_contigs(self, genomes=None):
"""
Compiles a list of genomes with missing and unvalidated sequences
and uploads them to Blazegraph.
"""
list_of_genomes = []
if not genomes:
list_of_genomes = find_missing_sequences()
else:
list_of_genomes = genomes
# find missing_sequences() returns a list of two-tuples (genome, accession number)
for (genome, accession) in list_of_genomes:
contigswrapper = ContigsWrapper(genome, accession)
try:
self.get_seqdata(contigswrapper)
if contigswrapper.dict["is_from"] == "PLASMID":
self.upload(contigswrapper, self.plasmid_rdf)
else:
SequenceValidator(contigswrapper).validate()
self.upload(contigswrapper, self.nonplasmid_rdf)
gc.collect()
except TypeError:
self.error_logging(contigswrapper)
def upload_missing_sequences(self):
"""Compiles a list of genomes with missing and unvalidated sequences
and uploads them to Blazegraph.
"""
for (genome, accession) in find_missing_sequences():
seqdata = SequenceMetadata(genome, accession)
try:
self.load_sequence(seqdata)
if seqdata.dict["is_from"] == "PLASMID":
self.upload(seqdata, self.plasmid_rdf)
else:
SequenceValidator(seqdata).validate()
self.upload(seqdata, self.nonplasmid_rdf)
gc.collect()
except TypeError:
self.error_logging(seqdata)
