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_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_edgecase_single_base_exon(self):
""" Example where the first exon is only one basepair long
"""
conn, cursor = get_db_cursor()
build = "toy_build"
location_dict = talon.make_location_dict(build, cursor)
run_info = talon.init_run_info(cursor, 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_beyond_cutoff_distance(self):
""" Example where the only nearby vertices are beyond the cutoff
distance, prompting creation of a new vertex."""
conn, cursor = get_db_cursor()
build = "toy_build"
location_dict = talon.make_location_dict(build, cursor)
run_info = talon.init_run_info(cursor, build)
conn.close()
chrom = "chr1"
pos = [1700, 1500, 1000, 900]
start = pos[0]
splice_pos = pos[1]
run_info.cutoff_5p = 250
strand = "-"
vertex_match, diff = talon.permissive_vertex_search(
chrom, start, strand, splice_pos, "start", location_dict, run_info)
assert vertex_match == None
assert diff == None
def test_match_at_cutoff_distance(self):
""" Example where the correct match is exactly the length of the cutoff
away from the position """
conn, cursor = get_db_cursor()
build = "toy_build"
location_dict = talon.make_location_dict(build, cursor)
run_info = talon.init_run_info(cursor, build)
chrom = "chr1"
pos = [1750, 1500, 1000, 900]
start = pos[0]
splice_pos = pos[1]
cutoff = 250
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, 2000, cursor)
assert diff == 250
conn.close()