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()
