def test_gene_annot(self):
""" Try to add gene annotation entries to database in batches
"""
conn, cursor = get_db_cursor()
build = "toy_build"
annot = [(1, "toy", "TALON", "status", "NOVEL"),
(2, "toy", "TALON", "status", "NOVEL")]
# Write observed to file
os.system("mkdir -p scratch/db_updates/")
with open("scratch/db_updates/gene_annot.tsv", 'w') as f:
for entry in annot:
f.write("\t".join([str(x) for x in entry]) + "\n")
batch_size = 1
talon.batch_add_annotations(cursor,
"scratch/db_updates/gene_annot.tsv",
"gene", batch_size)
# Test if items are there
query = "SELECT * FROM gene_annotations WHERE value = 'NOVEL'"
cursor.execute(query)
assert len(cursor.fetchall()) == 2
conn.close()
def test_exon_annot(self):
""" Try to add exon annotation entries to database in batches
"""
conn, cursor = get_db_cursor()
build = "toy_build"
edge_dict = talon.make_edge_dict(cursor)
run_info = talon.init_run_info(cursor, build)
annot = [(1, "toy", "TALON", "status", "NOVEL"),
(2, "toy", "TALON", "status", "NOVEL")]
batch_size = 3
talon.batch_add_annotations(cursor, annot, "exon", batch_size)
# Test if items are there
query = "SELECT * FROM exon_annotations WHERE value = 'NOVEL'"
cursor.execute(query)
assert len(cursor.fetchall()) == 2
conn.close()