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_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_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_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_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_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_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_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_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_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_NNC_type_match(self):
""" Example where some vertices match a gene, while others don't.
"""
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, 200, 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_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_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_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_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_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_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()
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_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()
