def test_genomic_unspliced(self): """ Monoexonic fragment that overlaps gene 1 """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) talon.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr1" strand = "+" positions = (1, 990) annotation = talon.identify_monoexon_transcript( chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) novelty_types = [x[-2] for x in annotation['transcript_novelty']] assert annotation['gene_ID'] == correct_gene_ID assert "genomic_transcript" in novelty_types assert annotation['end_delta'] == -10 conn.close()
def test_antisense(self): """ Example where the transcript is antisense """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) talon.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr4" strand = "+" positions = (1300, 3900) annotation = talon.identify_monoexon_transcript( chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) anti_gene_ID = fetch_correct_ID("TG6", "gene", cursor) gene_novelty_types = [x[-2] for x in annotation['gene_novelty']] t_novelty_types = [x[-2] for x in annotation['transcript_novelty']] assert annotation['gene_novelty'][0][-1] == "TRUE" assert "antisense_gene" in gene_novelty_types assert "antisense_transcript" in t_novelty_types conn.close()
def test_spliced_antisense(self): """ Example where the transcript matches known vertices but is antisense """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr2" strand = "-" positions = [1000, 900, 600, 500, 100, 1] annotation = talon.identify_transcript(chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) anti_gene_ID = fetch_correct_ID("TG2", "gene", cursor) gene_novelty_types = [x[-2] for x in annotation['gene_novelty']] t_novelty_types = [x[-2] for x in annotation['transcript_novelty']] assert annotation['gene_novelty'][0][-1] == "TRUE" assert "antisense_gene" in gene_novelty_types assert "antisense_transcript" in t_novelty_types assert annotation['start_delta'] == annotation['end_delta'] == 0 conn.close()
def test_match(self): """ Example where the transcript is a moniexonic match. """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) talon.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr4" strand = "-" positions = (3900, 1100) annotation = talon.identify_monoexon_transcript( chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG6", "gene", cursor) correct_transcript_ID = fetch_correct_ID("TG6-001", "transcript", cursor) assert annotation['gene_ID'] == correct_gene_ID assert annotation['start_delta'] == 100 assert annotation['end_delta'] == -100 conn.close()
def test_ISM_internal(self): """ Example where the transcript matches an internal exon """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) talon.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr1" strand = "+" positions = (500, 600) annotation = talon.identify_monoexon_transcript( chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) novelty_types = [x[-2] for x in annotation['transcript_novelty']] assert annotation['gene_ID'] == correct_gene_ID assert "ISM_transcript" in novelty_types assert annotation['start_delta'] == annotation['end_delta'] == 0 conn.close()
def test_NIC_instead_of_ISM(self): """ Test case where the transcript looks like an ISM, but is NIC on account of having known starts and ends """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr3" strand = "+" positions = (800, 1000, 1200, 1400, 1600, 1800, 2000, 2200) annotation = talon.identify_transcript(chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG5", "gene", cursor) novelty_types = [x[-2] for x in annotation['transcript_novelty']] assert annotation['gene_ID'] == correct_gene_ID assert "NIC_transcript" in novelty_types conn.close()
def test_partial_match_3prime(self): """ Example where the transcript is short, so it overlaps the annotated transcript but is not an accepted match. the end should get assigned to the annotated end, but the end is novel """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) talon.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr4" strand = "-" positions = (2000, 1100) annotation = talon.identify_monoexon_transcript( chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG6", "gene", cursor) assert annotation['gene_ID'] == correct_gene_ID assert annotation['start_delta'] == None assert annotation['end_delta'] == -100 conn.close()
def test_FSM_perfect(self): """ Example where the transcript is a perfect full splice match. """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr1" strand = "+" positions = [1, 100, 500, 600, 900, 1000] annotation = talon.identify_transcript(chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) correct_transcript_ID = fetch_correct_ID("TG1-001", "transcript", cursor) assert annotation['gene_ID'] == correct_gene_ID assert annotation['transcript_ID'] == correct_transcript_ID assert annotation['transcript_novelty'] == [] conn.close()
def test_FSM_end_diff(self): """ Example where the transcript is an FSM but has a difference on the ends large enough to be novel. """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr2" strand = "+" positions = [1, 100, 500, 600, 900, 1500] annotation = talon.identify_transcript(chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG2", "gene", cursor) novelty_types = [x[-2] for x in annotation['transcript_novelty']] assert annotation['gene_ID'] == correct_gene_ID assert annotation['end_delta'] == None conn.close()
def test_NNC(self): """ Example where the transcript skips an exon and has a novel splice donor """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr1" strand = "+" positions = [1, 50, 900, 1000] annotation = talon.identify_transcript(chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) novelty_types = [x[-2] for x in annotation['transcript_novelty']] assert annotation['gene_ID'] == correct_gene_ID assert "NNC_transcript" in novelty_types assert annotation['start_delta'] == annotation['end_delta'] == 0 conn.close()
def test_antisense(self): """ Example where the vertices are known but there is no same-strand match """ conn, cursor = get_db_cursor() build = "toy_build" edge_dict = talon.make_edge_dict(cursor) locations = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) # Construct temp novel gene db talon.make_temp_novel_gene_table(cursor, "toy_build") chrom = "chr1" start = 1000 end = 1 edge_IDs = [run_info.edge + 1] positions = [1000, 900, 100, 1] vertex_IDs = [5, 2] strand = "-" anti_strand = "+" v_novelty = (0, 0, 0, 0) # Find antisense match gene_ID, transcript_ID, gene_novelty, transcript_novelty, start_end_info = \ talon.process_spliced_antisense(chrom, positions, strand, edge_IDs, vertex_IDs, transcript_dict, gene_starts, gene_ends, edge_dict, locations, vertex_2_gene, run_info, cursor) #anti_gene_ID = talon.find_gene_match_on_vertex_basis(vertex_IDs, # anti_strand, # vertex_2_gene) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) anti_gene_ID = gene_novelty[-1][-1] assert anti_gene_ID == correct_gene_ID assert start_end_info["vertex_IDs"] == [6, 5, 2, 1] conn.close()
def test_no_match(self): """ Example where no match exists """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, "toy_build") run_info = talon.init_run_info(cursor, build) vertex2gene = talon.make_vertex_2_gene_dict(cursor) vertex_IDs = (1000, 2000, 3000, 4000) strand = "+" gene_ID = talon.find_gene_match_on_vertex_basis( vertex_IDs, strand, vertex2gene) assert gene_ID == None conn.close()
def test_single_match(self): """ Example where the interval overlaps exactly one gene """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, "toy_build") location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) chrom = "chr1" pos = [0, 1500] strand = "+" gene_ID, match_strand = talon.search_for_overlap_with_gene( chrom, pos[0], pos[1], strand, cursor, run_info) assert gene_ID == fetch_correct_ID("TG1", "gene", cursor) assert match_strand == strand conn.close()
def test_create_temp_table(self): """ Create the table and make sure it is accessible even if it is empty, and make sure it doesn't clash with the TALON database """ # Open TALON database at the same time conn, cursor = get_db_cursor() build = "toy_build" # Now run the temp table creation talon.make_temp_novel_gene_table(cursor, build) try: query = """SELECT * FROM temp_gene""" cursor.execute(query) results = cursor.fetchall() except: pytest.fail("Something went wrong with temp table query") conn.close()
def test_perfect_match(self): """ Example where the vertices perfectly match a gene. """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, "toy_build") run_info = talon.init_run_info(cursor, build) vertex2gene = talon.make_vertex_2_gene_dict(cursor) vertex_IDs = (1, 2, 3, 4, 5, 6) strand = "+" gene_ID = talon.find_gene_match_on_vertex_basis( vertex_IDs, strand, vertex2gene) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) assert gene_ID == correct_gene_ID conn.close()
def test_gene_update(self): """ Try to add novel gene entries to database while ignoring duplicates """ conn, cursor = get_db_cursor() build = "toy_build" edge_dict = talon.make_edge_dict(cursor) run_info = talon.init_run_info(cursor, build) talon.make_temp_novel_gene_table(cursor, build) talon.create_gene("chr4", 1, 1000, "+", cursor, run_info) talon.add_genes(cursor) # Test if gene with ID 6 is there, but make sure we didn't add # duplicates of the other genes query = "SELECT * FROM genes" gene_IDs = [x['gene_ID'] for x in cursor.execute(query)] assert 7 in gene_IDs assert len(gene_IDs) == 7 conn.close()
def test_same_strand_match_left_overlap(self): """ Example where the overlap is on the same strand. Query start is to the left of the gene, and query end is before the end of the gene. """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, "toy_build") location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) chrom = "chr1" pos = [550, 1700] strand = "-" gene_ID, match_strand = talon.search_for_overlap_with_gene( chrom, pos[0], pos[1], strand, cursor, run_info) assert gene_ID == fetch_correct_ID("TG3", "gene", cursor) assert match_strand == strand conn.close()
def test_same_strand_match_with_two_genes(self): """ Example where interval overlaps two genes, one of which is on the same strand. """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, "toy_build") location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) chrom = "chr1" pos = [1500, 910] strand = "-" gene_ID, match_strand = talon.search_for_overlap_with_gene( chrom, pos[0], pos[1], strand, cursor, run_info) assert gene_ID == fetch_correct_ID("TG3", "gene", cursor) assert match_strand == strand conn.close()
def test_antisense_match(self): """ Example where interval overlaps one gene in the antisense direction. """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, "toy_build") location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) chrom = "chr1" pos = [1400, 2100] strand = "+" gene_ID, match_strand = talon.search_for_overlap_with_gene( chrom, pos[0], pos[1], strand, cursor, run_info) assert gene_ID == fetch_correct_ID("TG3", "gene", cursor) assert match_strand == "-" conn.close()
def test_2_genes_same_strand(self): """ Example where query overlaps two genes. Must choose the one with more overlap """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, "toy_build") location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) chrom = "chr1" pos = [800, 5050] strand = "+" gene_ID, match_strand = talon.search_for_overlap_with_gene( chrom, pos[0], pos[1], strand, cursor, run_info) assert gene_ID == fetch_correct_ID("TG1", "gene", cursor) assert match_strand == "+" conn.close()
def test_overlap_but_no_vertex_match(self): """ Example where the transcript is short, so it overlaps the annotated transcript but is not an accepted match. the start should get assigned to the annotated end, but the end is novel """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, build) talon.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) tot_vertices = len(vertex_2_gene) query = """ SELECT COUNT(*) FROM temp_monoexon """ tot_monoexonic = cursor.execute(query).fetchone()[0] chrom = "chr4" strand = "-" positions = (2500, 2000) annotation = talon.identify_monoexon_transcript( chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) correct_gene_ID = fetch_correct_ID("TG6", "gene", cursor) print(annotation['start_vertex']) print(annotation['end_vertex']) assert annotation['gene_ID'] == correct_gene_ID assert annotation['start_delta'] == None assert annotation['end_delta'] == None # Now check if the transcript got added to the right data structures assert len(vertex_2_gene) == tot_vertices + 2 assert cursor.execute(query).fetchone()[0] == tot_monoexonic + 1 conn.close()
def test_no_match(self): """ Example where the supplied interval should not match anything """ conn, cursor = get_db_cursor() build = "toy_build" talon.make_temp_novel_gene_table(cursor, "toy_build") location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) chrom = "chr1" pos = [3000, 4000] strand = "+" gene_ID, match_strand = talon.search_for_overlap_with_gene( chrom, pos[0], pos[1], strand, cursor, run_info) assert gene_ID == None # Should get same results for flipped interval gene_ID, match_strand = talon.search_for_overlap_with_gene( chrom, pos[0], pos[1], strand, cursor, run_info) assert gene_ID == None conn.close()
def test_NIC_with_all_known_edges(self): """ Test case derived from a real mouse Map2k4 read. All of edges are known (except 3'), yet the read is NIC not FSM/ISM """ conn = sqlite3.connect("scratch/Map2k4.db") conn.row_factory = sqlite3.Row cursor = conn.cursor() build = "mm10" talon.make_temp_novel_gene_table(cursor, build) edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) chrom = "chr11" strand = "-" positions = [ 65788254, 65788136, 65775765, 65775733, 65756371, 65756269, 65735366, 65735192, 65719603, 65719484, 65712297, 65712178, 65709983, 65709932, 65707111, 65706984, 65696365, 65696288, 65693570, 65693422, 65691773, 65691728, 65690804, 65689322 ] annotation = talon.identify_transcript(chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info) assert annotation['gene_ID'] == 1 assert annotation['transcript_ID'] == 8 novelty_types = [x[-2] for x in annotation['transcript_novelty']] assert "NIC_transcript" in novelty_types conn.close()
def test_intergenic(self): """ Example where the transcript is an NIC match to an existing one by virtue of a new splice donor. """ conn, cursor = get_db_cursor() build = "toy_build" edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) correct_gene_ID = run_info.genes + 1 # Construct temp novel gene db talon.make_temp_novel_gene_table(cursor, "toy_build") chrom = "chrX" positions = [1, 100, 900, 1000] edge_IDs = [run_info.edge + 1, run_info.edge + 2] vertex_IDs = [run_info.vertex + 1, run_info.vertex + 2] strand = "+" gene_ID, transcript_ID, gene_novelty, transcript_novelty, start_end_info = \ talon.process_remaining_mult_cases(chrom, positions, strand, edge_IDs, vertex_IDs, transcript_dict, gene_starts, gene_ends, edge_dict, location_dict, vertex_2_gene, run_info, cursor) assert gene_ID == correct_gene_ID assert transcript_dict[frozenset(start_end_info["edge_IDs"])] != None assert gene_novelty[0][-2] == "intergenic_novel" conn.close()
def test_genomic(self): """ Example where the transcript overlaps a gene but contains no known splice vertices """ conn, cursor = get_db_cursor() build = "toy_build" edge_dict = talon.make_edge_dict(cursor) location_dict = talon.make_location_dict(build, cursor) run_info = talon.init_run_info(cursor, build) transcript_dict = talon.make_transcript_dict(cursor, build) vertex_2_gene = talon.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = talon.make_gene_start_and_end_dict( cursor, build) # Construct temp novel gene db talon.make_temp_novel_gene_table(cursor, "toy_build") chrom = "chr1" positions = [1000, 950, 700, 600] edge_IDs = [run_info.edge + 1, run_info.edge + 2] vertex_IDs = [run_info.vertex + 1, run_info.vertex + 2] strand = "-" gene_ID, transcript_ID, gene_novelty, transcript_novelty, start_end_info = \ talon.process_remaining_mult_cases(chrom, positions, strand, edge_IDs, vertex_IDs, transcript_dict, gene_starts, gene_ends, edge_dict, location_dict, vertex_2_gene, run_info, cursor) correct_gene_ID = fetch_correct_ID("TG3", "gene", cursor) assert gene_ID == correct_gene_ID assert transcript_dict[frozenset(start_end_info["edge_IDs"])] != None assert gene_novelty == [] assert transcript_novelty[-1][-2] == "genomic_transcript" conn.close()