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)