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"
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)
orig_vertices = run_info['vertex']
gene_starts, gene_ends = talon.make_gene_start_and_end_dict(
cursor, build)
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()
def test_no_match(self):
""" Example with no FSM match """
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)
gene_starts, gene_ends = talon.make_gene_start_and_end_dict(
cursor, build)
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_FSM_perfect(self):
""" Example where the transcript is a perfect full splice match.
"""
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)
gene_starts, gene_ends = talon.make_gene_start_and_end_dict(
cursor, build)
chrom = "chr1"
positions = [1, 100, 500, 600, 900, 1010]
strand = "+"
edge_IDs = [2, 3, 4]
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)
correct_gene_ID = fetch_correct_ID("TG1", "gene", cursor)
correct_transcript_ID = fetch_correct_ID("TG1-001", "transcript",
cursor)
assert gene_ID == correct_gene_ID
assert transcript_ID == correct_transcript_ID
assert novelty == []
assert start_end_info["start_vertex"] == 1
assert start_end_info["end_vertex"] == 6
assert start_end_info["diff_3p"] == 10
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"
db = "scratch/toy.db"
talon.get_counters(db)
orig_vertices = talon.vertex_counter.value()
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 = "chr2"
positions = [1, 100, 500, 600, 900,
1301] #Last position is > 300bp away
strand = "+"
edge_IDs = [13, 14, 15]
vertex_IDs = [14, 15, 16, 17]
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)
correct_gene_ID = fetch_correct_ID("TG2", "gene", cursor)
correct_transcript_ID = fetch_correct_ID("TG2-001", "transcript",
cursor)
assert gene_ID == correct_gene_ID
assert transcript_ID == correct_transcript_ID
assert start_end_info["end_vertex"] == orig_vertices + 1
conn.close()