def test_antisense(self):
""" Example where all of the vertices are in the database, but the edges
are not, because they are antisense to the original transcript """
conn, cursor = get_db_cursor()
build = "toy_build"
edge_dict = talon.make_edge_dict(cursor)
run_info = talon.init_run_info(cursor, build)
orig_n_edges = len(edge_dict)
conn.close()
chrom = "chr2"
vertex_IDs = [13, 12, 11, 10]
strand = "-"
edge_IDs, novelty = talon.match_all_splice_edges(
vertex_IDs, strand, edge_dict, run_info)
expected_edges = []
for i in range(1, 4):
num = orig_n_edges + i
edge_id = num
expected_edges.append(edge_id)
assert edge_IDs == expected_edges
assert novelty == [1, 1, 1]
def test_all_known_edges(self):
""" Example where the toy transcript database contains matches for all
vertices.
"""
conn, cursor = get_db_cursor()
build = "toy_build"
edge_dict = talon.make_edge_dict(cursor)
run_info = talon.init_run_info(cursor, build)
conn.close()
chrom = "chr1"
vertex_IDs = [2, 3, 4, 5]
strand = "+"
edge_IDs, novelty = talon.match_all_splice_edges(
vertex_IDs, strand, edge_dict, run_info)
assert edge_IDs == [2, 3, 4]
assert novelty == [0, 0, 0]