def test_dist_even_mixture():
with microhapulator.open(data_file("murica/x-obs-genotype.json"),
"r") as fh:
p1 = TypingResult(fh)
p2 = SimulatedProfile.populate_from_bed(
data_file("murica/x-sim-genotype.bed"))
assert mhapi.dist(p1, p2) == 0
assert p1 == p2
def test_haplotypes():
simprof = SimulatedProfile.populate_from_bed(data_file("gttest.bed.gz"))
typeprof = TypingResult(fromfile=data_file("prof/gttest.json"))
assert simprof.haplotypes("BoGuSlOcUs") == set()
assert typeprof.haplotypes("BoGuSlOcUs") == set()
assert simprof.haplotypes("MHDBL000135") == set(["G,C,T", "G,T,C"])
assert typeprof.haplotypes("MHDBL000135") == set(["G,C,T", "G,T,C"])
assert simprof.haplotypes("MHDBL000135", index=0) == set(["G,C,T"])
assert simprof.haplotypes("MHDBL000135", index=1) == set(["G,T,C"])
assert typeprof.haplotypes("MHDBL000135", index=0) == set()
def test_sim_obs_profile_not_equal():
simprof1 = SimulatedProfile.populate_from_bed(
data_file("gttest-mismatch1.bed.gz"))
assert simprof1 is not None
assert simprof1 != 42
assert simprof1 != 3.14159
assert simprof1 != "A,C,C,T"
typeprof1 = TypingResult(fromfile=data_file("prof/gttest.json"))
assert simprof1 != typeprof1
assert typeprof1 != simprof1
assert typeprof1 != 1985
assert typeprof1 != 98.6
simprof2 = SimulatedProfile.populate_from_bed(
data_file("gttest-mismatch2.bed.gz"))
assert simprof1 != simprof2
assert simprof2 != typeprof1
assert typeprof1 != simprof2
typeprof2 = TypingResult(fromfile=data_file("prof/gttest-altered.json"))
assert typeprof1 != typeprof2
def test_dist_log_mixture():
p1 = TypingResult(data_file("murica/y-obs-genotype.json"))
p2 = SimulatedProfile.populate_from_bed(
data_file("murica/y-sim-genotype.bed"))
assert mhapi.dist(p1, p2) == 19
assert p1 != p2
def test_sim_obs_profile_equality():
simprof = SimulatedProfile.populate_from_bed(data_file("gttest.bed.gz"))
typeprof = TypingResult(fromfile=data_file("prof/gttest.json"))
assert simprof == typeprof
assert typeprof == simprof
def test_haploindexes():
simprof = SimulatedProfile.populate_from_bed(
data_file("gttest-mismatch1.bed.gz"))
assert simprof.haploindexes() == set([0, 1])
typeprof = TypingResult(data_file("pashtun-sim/test-output.json"))
assert typeprof.haploindexes() == set()