def load_clusterblast_database(seq_record, searchtype="general"):
accessiondict = {}
for cds in utils.get_cds_features(seq_record):
accessiondict[utils.get_gene_acc(cds)] = utils.get_gene_accession(cds)
clusters = load_geneclusters(searchtype)
proteins = load_geneclusterproteins(accessiondict, searchtype)
return clusters, proteins
def load_clusterblast_database(seq_record, searchtype="general"):
options = config.get_config()
accessiondict = {}
for cds in utils.get_cds_features(seq_record):
accessiondict[utils.get_gene_acc(cds)] = utils.get_gene_accession(cds)
clusters = load_geneclusters(searchtype)
proteinlocations, proteinstrands, proteinannotations, proteintags = load_geneclusterproteins(accessiondict, searchtype)
return clusters, proteinlocations, proteinstrands, proteinannotations, proteintags
def test_get_gene_accession_no_id(self):
"Test utils.get_gene_accession() without available id"
feature = FakeFeature("CDS")
self.assertEqual('no_tag_found', utils.get_gene_accession(feature))
def test_get_gene_accession_gene(self):
"Test utils.get_gene_accession() with gene"
feature = FakeFeature("CDS")
feature.qualifiers['gene'] = ['fake007']
self.assertEqual('fake007', utils.get_gene_accession(feature))
def test_get_gene_accession_locus(self):
"Test utils.get_gene_accession() with locus_tag"
feature = FakeFeature("CDS")
feature.qualifiers['locus_tag'] = ['fake007']
self.assertEqual('fake007', utils.get_gene_accession(feature))
def test_get_gene_accession_protein(self):
"Test utils.get_gene_accession() with protein_id"
feature = FakeFeature("CDS")
feature.qualifiers['protein_id'] = ['fake007']
self.assertEqual('fake007', utils.get_gene_accession(feature))
