def test_match_monoexonic(self): """ Test the permissive match strategy on a monoexonic transcript """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) chrom = "chr2" pos = [920, 970] start = pos[0] splice_pos = pos[1] run_info.cutoff_5p = 500 run_info.cutoff_3p = 500 strand = "+" start_match, start_diff = talon.permissive_vertex_search( chrom, start, strand, splice_pos, "start", location_dict, run_info) end = pos[1] splice_pos = pos[0] end_match, end_diff = talon.permissive_vertex_search( chrom, end, strand, splice_pos, "end", location_dict, run_info) assert start_match == fetch_correct_vertex_ID(chrom, 900, cursor) assert start_diff == 20 assert end_match == fetch_correct_vertex_ID(chrom, 1000, cursor) assert end_diff == -30 conn.close()
def test_with_novel_location(self): """ Example where the toy transcript database contains a novel position. """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" talon.get_counters(database) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) orig_vertex_count = talon.vertex_counter.value() orig_n_locations = len(location_dict["chr1"]) conn.close() chrom = "chr1" strand = "+" pos = [1, 150, 500, 600, 900, 1000] vertex_IDs, novelty = talon.match_splice_vertices(chrom, pos, strand, location_dict, run_info) # Make sure that no match got returned new_vertex_count = talon.vertex_counter.value() assert vertex_IDs == [ new_vertex_count, 3, 4, 5] # Make sure the data structures got updated assert new_vertex_count == orig_vertex_count + 1 assert len(location_dict["chr1"]) == orig_n_locations + 1
def test_monoexonic_edge_case(self): """ Case I observed during testing where start and end accidentally ended up being assigned to the same vertex """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) chrom = "chr1" pos = [550, 610] start = pos[0] splice_pos = pos[1] run_info.cutoff_5p = 500 run_info.cutoff_3p = 500 strand = "+" start_match, start_diff = talon.permissive_vertex_search( chrom, start, strand, splice_pos, "start", location_dict, run_info) end = pos[1] splice_pos = pos[0] end_match, end_diff = talon.permissive_vertex_search( chrom, end, strand, splice_pos, "end", location_dict, run_info) assert start_match == 3 assert end_match == 4
def test_ISM_prefix(self): """ Example where the transcript is a prefix ISM with a novel start """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" run_info = talon.init_run_info(database, build) talon.get_counters(database) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) transcript_dict = init_refs.make_transcript_dict(cursor, build) gene_starts, gene_ends = init_refs.make_gene_start_and_end_dict( cursor, build) chrom = "chr1" strand = "+" positions = [1, 100, 500, 600] edge_IDs = [2] vertex_IDs = [2, 3] v_novelty = [0, 0] all_matches = talon.search_for_ISM(edge_IDs, transcript_dict) gene_ID, transcript_ID, novelty, start_end_info = talon.process_ISM( chrom, positions, strand, edge_IDs, vertex_IDs, all_matches, transcript_dict, gene_starts, gene_ends, edge_dict, location_dict, run_info) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) assert gene_ID == correct_gene_ID assert start_end_info["vertex_IDs"] == [1, 2, 3, 4] assert start_end_info["edge_IDs"] == [1, 2, 3] 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" database = "scratch/toy.db" talon.get_counters(database) init_refs.make_temp_novel_gene_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = init_refs.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, "tmp_gene") 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_FSM_perfect(self): """ Example where the transcript is a perfect full splice match. """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" talon.get_counters(database) init_refs.make_temp_novel_gene_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = init_refs.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, "temp_gene") 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_no_match(self): """ Example with no ISM match """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" run_info = talon.init_run_info(database, build) talon.get_counters(database) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) transcript_dict = init_refs.make_transcript_dict(cursor, build) gene_starts, gene_ends = init_refs.make_gene_start_and_end_dict( cursor, build) chrom = "chr1" strand = "+" positions = [1, 100, 900, 1000] edge_IDs = [200] vertex_IDs = [2, 5] v_novelty = [0, 0] all_matches = talon.search_for_ISM(edge_IDs, transcript_dict) assert all_matches == None 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" database = "scratch/toy.db" talon.get_counters(database) init_refs.make_temp_novel_gene_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = init_refs.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, "temp_gene") 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" database = "scratch/toy.db" talon.get_counters(database) init_refs.make_temp_novel_gene_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = init_refs.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, "temp_gene") 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_genomic_unspliced(self): """ Monoexonic fragment that overlaps gene 1 """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" talon.get_counters(database) init_refs.make_temp_novel_gene_table(cursor, build) init_refs.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = init_refs.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, "temp_gene", "temp_monoexon") 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_match(self): """ Example where the transcript is a monoexonic match. """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" talon.get_counters(database) init_refs.make_temp_novel_gene_table(cursor, build) init_refs.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts = init_refs.make_gene_start_or_end_dict(cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") 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, 'temp_gene', 'temp_monoexon') 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_NNC_match(self): """ Example where the transcript is an NNC match to an existing one by virtue of a new splice donor. """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" talon.get_counters(database) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts = init_refs.make_gene_start_or_end_dict( cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") chrom = "chr1" positions = [1, 110, 900, 1000] edge_IDs = [talon.edge_counter.value() + 1] vertex_IDs = [talon.vertex_counter.value() + 1, 5] strand = "+" v_novelty = [0, 0] gene_ID, transcript_ID, transcript_novelty, start_end_info = talon.process_NNC( chrom, positions, strand, edge_IDs, vertex_IDs, transcript_dict, gene_starts, gene_ends, edge_dict, location_dict, vertex_2_gene, run_info) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) assert gene_ID == correct_gene_ID assert start_end_info["vertex_IDs"] == [1] + vertex_IDs + [6] assert transcript_dict[frozenset(start_end_info["edge_IDs"])] != None conn.close()
def test_no_match(self): """ Example with no FSM match """ conn, cursor = get_db_cursor() build = "toy_build" db = "scratch/toy.db" talon.get_counters(db) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(db, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) gene_starts = init_refs.make_gene_start_or_end_dict( cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") chrom = "chr1" positions = [1, 100, 500, 600] strand = "+" edge_IDs = [2] vertex_IDs = [2, 3, 4, 5] v_novelty = [0, 0, 0, 0] all_matches = talon.search_for_ISM(edge_IDs, transcript_dict) gene_ID, transcript_ID, novelty, start_end_info = talon.process_FSM( chrom, positions, strand, edge_IDs, vertex_IDs, all_matches, gene_starts, gene_ends, edge_dict, location_dict, run_info) assert gene_ID == transcript_ID == None conn.close()
def test_antisense(self): """ Example where the transcript is antisense """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" talon.get_counters(database) init_refs.make_temp_novel_gene_table(cursor, build) init_refs.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = init_refs.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, 'temp_gene', 'temp_monoexon') 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_find_match(self): """ Example where the toy transcript edge dict does not contain the edge being queried. """ conn, cursor = get_db_cursor() # Create a location dict and then fetch vertices for two psotions build = "toy_build" location_dict = init_refs.make_location_dict(build, cursor) edge_dict = init_refs.make_edge_dict(cursor) conn.close() chrom = "chr1" pos1 = 600 pos2 = 500 v1 = talon.search_for_vertex_at_pos(chrom, pos1, location_dict)["location_ID"] v2 = talon.search_for_vertex_at_pos(chrom, pos2, location_dict)["location_ID"] assert v1 != None assert v2 != None # Now look for the edge between them edge_match = talon.search_for_edge(v1, v2, "exon", edge_dict) assert edge_match == None # Try them in the opposite order edge_match = talon.search_for_edge(v2, v1, "exon", edge_dict) assert edge_match["edge_ID"] == 3
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" database = "scratch/toy.db" talon.get_counters(database) edge_dict = init_refs.make_edge_dict(cursor) locations = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts = init_refs.make_gene_start_or_end_dict( cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") # Construct temp novel gene db init_refs.make_temp_novel_gene_table(cursor, "toy_build") chrom = "chr1" start = 1000 end = 1 edge_IDs = [talon.edge_counter.value() + 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, "temp_gene") #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_find_no_match(self): """ Example where the toy transcript database contains no matches for the position. """ conn, cursor = get_db_cursor() build = "toy_build" location_dict = init_refs.make_location_dict(build, cursor) chrom = "chr1" pos = 0 vertex_match = talon.search_for_vertex_at_pos(chrom, pos, location_dict) conn.close() # Make sure that no match got returned assert vertex_match == None
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" database = "scratch/toy.db" talon.get_counters(database) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts = init_refs.make_gene_start_or_end_dict( cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") # Construct temp novel gene db init_refs.make_temp_novel_gene_table(cursor, "toy_build") chrom = "chr1" positions = [1000, 950, 700, 600] edge_IDs = [ talon.edge_counter.value() + 1, talon.edge_counter.value() + 2 ] vertex_IDs = [ talon.vertex_counter.value() + 1, talon.vertex_counter.value() + 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, "temp_gene") 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()
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" database = "scratch/toy.db" talon.get_counters(database) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts = init_refs.make_gene_start_or_end_dict( cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") correct_gene_ID = talon.gene_counter.value() + 1 # Construct temp novel gene db init_refs.make_temp_novel_gene_table(cursor, "toy_build") chrom = "chrX" positions = [1, 100, 900, 1000] edge_IDs = [ talon.edge_counter.value() + 1, talon.edge_counter.value() + 2 ] vertex_IDs = [ talon.vertex_counter.value() + 1, talon.vertex_counter.value() + 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, "temp_gene") 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_find_exactly_one_match(self): """ Example where the toy transcript database contains exactly one match for the position. """ conn, cursor = get_db_cursor() build = "toy_build" location_dict = init_refs.make_location_dict(build, cursor) chrom = "chr1" pos = 1 match = talon.search_for_vertex_at_pos(chrom, pos, location_dict) conn.close() print(match) # Make sure that match is correct and that we can access various # attributes using their names assert match["genome_build"] == "toy_build" assert match["chromosome"] == "chr1" assert match["position"] == 1
def test_single_match(self): """ Example where the interval overlaps exactly one gene """ conn, cursor = get_db_cursor() database = "scratch/toy.db" build = "toy_build" init_refs.make_temp_novel_gene_table(cursor, "toy_build") location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build, tmp_dir="scratch/tmp/") 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, "temp_gene") assert gene_ID == fetch_correct_ID("TG1", "gene", cursor) assert match_strand == strand conn.close()
def test_ISM_suffix(self): """ Example where the transcript is an ISM with suffix """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" run_info = talon.init_run_info(database, build) talon.get_counters(database) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) transcript_dict = init_refs.make_transcript_dict(cursor, build) gene_starts = init_refs.make_gene_start_or_end_dict(cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") chrom = "chr1" strand = "+" positions = [ 500, 600, 900, 1000 ] edge_IDs = [4] vertex_IDs = [4, 5] v_novelty = [0, 0] all_matches = talon.search_for_ISM(edge_IDs, transcript_dict) gene_ID, transcript_ID, novelty, start_end_info = talon.process_ISM(chrom, positions, strand, edge_IDs, vertex_IDs, all_matches, transcript_dict, gene_starts, gene_ends, edge_dict, location_dict, run_info) correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor) assert gene_ID == correct_gene_ID assert start_end_info["vertex_IDs"] == [3, 4, 5, 6] assert start_end_info["edge_IDs"] == [3, 4, 5] assert start_end_info["start_novelty"] == 0 # because the exon is known assert start_end_info["end_novelty"] == 0 assert transcript_dict[frozenset(start_end_info["edge_IDs"])] != 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 """ database = "scratch/Map2k4.db" talon.get_counters(database) conn = sqlite3.connect(database) conn.row_factory = sqlite3.Row cursor = conn.cursor() build = "mm10" init_refs.make_temp_novel_gene_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts, gene_ends = init_refs.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, "temp_gene") 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_antisense_match(self): """ Example where interval overlaps one gene in the antisense direction. """ database = "scratch/toy.db" conn, cursor = get_db_cursor() build = "toy_build" init_refs.make_temp_novel_gene_table(cursor, "toy_build") location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, 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, "temp_gene") assert gene_ID == fetch_correct_ID("TG3", "gene", cursor) assert match_strand == "-" 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. """ database = "scratch/toy.db" conn, cursor = get_db_cursor() build = "toy_build" init_refs.make_temp_novel_gene_table(cursor, "toy_build") location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, 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, "temp_gene") 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. """ database = "scratch/toy.db" conn, cursor = get_db_cursor() build = "toy_build" init_refs.make_temp_novel_gene_table(cursor, "toy_build") location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, 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, "temp_gene") assert gene_ID == fetch_correct_ID("TG3", "gene", cursor) assert match_strand == strand conn.close()
def test_2_genes_same_strand(self): """ Example where query overlaps two genes. Must choose the one with more overlap """ database = "scratch/toy.db" conn, cursor = get_db_cursor() build = "toy_build" init_refs.make_temp_novel_gene_table(cursor, "toy_build") location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, 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, "temp_gene") assert gene_ID == fetch_correct_ID("TG1", "gene", cursor) assert match_strand == "+" conn.close()
def test_edgecase_single_base_exon(self): """ Example where the first exon is only one basepair long """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) chrom = "chr1" pos = [1, 1, 500, 600] start = pos[0] splice_pos = pos[2] cutoff = 500 strand = "+" vertex_match, diff = talon.permissive_vertex_search( chrom, start, strand, splice_pos, "start", location_dict, run_info) assert vertex_match == fetch_correct_vertex_ID(chrom, 1, cursor) assert diff == 0 conn.close()
def test_partial_match(self): """ Example where the transcript overlaps a single-exon transcript, but is shorter. In the past, the start would be assigned to the annotated start, and the end would be novel. This is no longer the case- at this time, the transcript will be assigned to the annotated match. """ conn, cursor = get_db_cursor() build = "toy_build" database = "scratch/toy.db" talon.get_counters(database) init_refs.make_temp_novel_gene_table(cursor, build) init_refs.make_temp_monoexonic_transcript_table(cursor, build) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(database, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) vertex_2_gene = init_refs.make_vertex_2_gene_dict(cursor) gene_starts = init_refs.make_gene_start_or_end_dict(cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") chrom = "chr4" strand = "-" positions = ( 3900, 2900 ) annotation = talon.identify_monoexon_transcript(chrom, positions, strand, cursor, location_dict, edge_dict, transcript_dict, vertex_2_gene, gene_starts, gene_ends, run_info, 'temp_gene', 'temp_monoexon') 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['transcript_ID'] == correct_transcript_ID assert annotation['start_delta'] == 100 assert annotation['end_delta'] == -1900 conn.close()
def test_FSM_start_diff(self): """ Example where the transcript is an FSM but has a difference on the start large enough to be novel. """ conn, cursor = get_db_cursor() build = "toy_build" db = "scratch/toy.db" talon.get_counters(db) edge_dict = init_refs.make_edge_dict(cursor) location_dict = init_refs.make_location_dict(build, cursor) run_info = talon.init_run_info(db, build) transcript_dict = init_refs.make_transcript_dict(cursor, build) orig_vertices = talon.vertex_counter.value() gene_starts = init_refs.make_gene_start_or_end_dict( cursor, build, "start") gene_ends = init_refs.make_gene_start_or_end_dict(cursor, build, "end") chrom = "chr1" positions = [2501, 1500, 1000, 900] #First postion is > 500bp away strand = "-" edge_IDs = [7] vertex_IDs = [7, 6] v_novelty = [0, 0] all_matches = talon.search_for_ISM(edge_IDs, transcript_dict) gene_ID, transcript_ID, novelty, start_end_info = talon.process_FSM( chrom, positions, strand, edge_IDs, vertex_IDs, all_matches, gene_starts, gene_ends, edge_dict, location_dict, run_info) correct_gene_ID = fetch_correct_ID("TG3", "gene", cursor) correct_transcript_ID = fetch_correct_ID("TG3-001", "transcript", cursor) assert gene_ID == correct_gene_ID assert transcript_ID == correct_transcript_ID assert start_end_info["start_vertex"] == orig_vertices + 1 assert start_end_info["end_vertex"] == 5 conn.close()