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_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_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_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_gene_update(self):
""" Try to add novel gene entries to database while ignoring duplicates
"""
conn, cursor = get_db_cursor()
build = "toy_build"
database = "scratch/toy.db"
run_info = talon.init_run_info(database, build)
talon.get_counters(database)
init_refs.make_temp_novel_gene_table(cursor, build)
talon.create_gene("chr4", 1, 1000, "+", cursor, "temp_gene")
# Write to file
os.system("mkdir -p scratch/db_updates/")
with open("scratch/db_updates/genes.tsv", 'w') as f:
cursor.execute("SELECT gene_ID, strand FROM temp_gene")
for entry in cursor.fetchall():
f.write("\t".join([str(x) for x in entry]) + "\n")
talon.batch_add_genes(cursor, "scratch/db_updates/genes.tsv", 10)
# 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_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_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_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_all(self):
""" Get all genes in the database """
conn, cursor = get_db_cursor()
build = "toy_build"
init_refs.make_temp_novel_gene_table(cursor, build)
# Count number of entries
cursor.execute(""" SELECT gene_ID FROM temp_gene """)
results = [x[0] for x in cursor.fetchall()]
conn.close()
assert results == [1, 2, 3, 4, 5, 6]
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_non_empty(self):
""" The specified interval contains one monoexonic transcript """
conn, cursor = get_db_cursor()
build = "toy_build"
init_refs.make_temp_novel_gene_table(cursor,
build,
chrom="chr1",
start=500,
end=1500)
cursor.execute(""" SELECT gene_ID FROM temp_gene """)
results = [x[0] for x in cursor.fetchall()]
conn.close()
assert results == [1, 2]
def test_no_match(self):
""" Example where no match exists """
conn, cursor = get_db_cursor()
db = "scratch/toy.db"
build = "toy_build"
init_refs.make_temp_novel_gene_table(cursor, "toy_build")
run_info = talon.init_run_info(db, build)
vertex2gene = init_refs.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_empty_interval(self):
""" The specified interval contains no monoexonic transcripts """
conn, cursor = get_db_cursor()
build = "toy_build"
init_refs.make_temp_novel_gene_table(cursor,
build,
chrom="chr1",
start=10000,
end=20000)
# Count number of entries
cursor.execute(""" SELECT gene_ID FROM temp_gene """)
assert cursor.fetchall() == []
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_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_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
init_refs.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()
db = "scratch/toy.db"
build = "toy_build"
init_refs.make_temp_novel_gene_table(cursor, "toy_build")
run_info = talon.init_run_info(db, build)
vertex2gene = init_refs.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_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_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_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_no_match(self):
""" Example where the supplied interval should not match anything
"""
conn, cursor = get_db_cursor()
build = "toy_build"
database = "scratch/toy.db"
run_info = talon.init_run_info(database, build, tmp_dir="scratch/tmp/")
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 = [3000, 4000]
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 == 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, "temp_gene")
assert gene_ID == None
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"
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 = [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,
"temp_gene")
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()
