def test_taxadumpparser_taxdump_noargs(self):
"""Check method runs ok"""
# Need connection to db. We use an empty db to fill list returned by
# parsing method
db = TaxaDB(dbtype='sqlite', dbname=self.testdb)
db.db.create_table(Taxa, safe=True)
dp = TaxaDumpParser(verbose=True, nodes_file=self.nodes,
names_file=self.names)
l = dp.taxdump()
self.assertEqual(len(l), 14)
def test_accessionparser_accession2taxid(self):
"""Check method yield correct number of entries read from accession
file"""
# Need connection to db. We use an empty db to fill list returned by
# parsing method
db = TaxaDB(dbtype='sqlite', dbname=self.testdb)
db.db.create_table(Taxa, safe=True)
db.db.create_table(Accession, safe=True)
# We need to load names.dmp and nodes.dmp
tp = TaxaDumpParser(nodes_file=self.nodes, names_file=self.names,
verbose=True)
taxa_info = tp.taxdump()
with db.db.atomic():
for i in range(0, len(taxa_info), self.chunk):
Taxa.insert_many(taxa_info[i:i + self.chunk]).execute()
ap = Accession2TaxidParser(acc_file=self.acc, chunk=self.chunk,
verbose=True)
acc_list = ap.accession2taxid()
total_entrires = 0
for accs in acc_list:
total_entrires += len(accs)
self.assertEqual(total_entrires, 55211)
def test_wrong_dbtype(self):
"""Check wrong dbtype raises an exception"""
with self.assertRaises(SystemExit):
TaxaDB(dbtype='fake')
def test_max_limit_ok(self):
ids = [i for i in range(1, 90)]
self.assertTrue(TaxaDB.check_list_ids(ids))
def test_max_limit_exceeded(self):
"""Check max length of ids raises an exception"""
ids = [i for i in range(1, 1001)]
with self.assertRaises(SystemExit):
TaxaDB.check_list_ids(ids)
def test_max_limit_ok(self):
ids = [i for i in range(1, 90)]
self.assertTrue(TaxaDB.check_list_ids(ids))
def test_max_limit_exceeded(self):
"""Check max length of ids raises an exception"""
ids = [i for i in range(1, 1001)]
with self.assertRaises(SystemExit):
TaxaDB.check_list_ids(ids)