def test_pipe_gbr_usc10(tmp_path):
hg38 = str(tmp_path / "hg38-placeholder.fasta")
copyfile(data_file("refr/usc10-refr.fna"), hg38)
run(["bwa", "index", hg38])
arglist = [
"pipe",
data_file("refr/usc10-refr.fna"),
data_file("def/usc10-offsets.tsv"),
data_file(""),
"gbr-usc",
"--workdir",
str(tmp_path),
"--threads",
"1",
"--hg38",
hg38,
]
args = microhapulator.cli.get_parser().parse_args(arglist)
microhapulator.cli.pipe.main(args)
expected = SimulatedProfile(fromfile=data_file("prof/gbr-usc10-sim.json"))
observed = TypingResult(fromfile=tmp_path / "analysis" / "gbr-usc" /
"gbr-usc-type.json")
diff = list(mhapi.diff(observed, expected))
assert len(diff) == 0
assert (tmp_path / "report.html").is_file()
expected = pd.read_csv(data_file("gbr-usc-summary.tsv"), sep="\t")
observed = pd.read_csv(tmp_path / "analysis" / "summary.tsv", sep="\t")
assert observed.equals(expected)
def test_diff_basic():
gt1 = SimulatedProfile(fromfile=data_file("prof/diff-comp-1.json"))
gt2 = SimulatedProfile(fromfile=data_file("prof/diff-comp-2.json"))
diff = list(mhapi.diff(gt1, gt2))
assert diff == [
("MHDBL000140", {"C,C,A,A"}, {"C,C,T,A"}),
("MHDBL000163", {"A,A,G,A,T"}, {"C,G,A,A,T"}),
]
def test_diff_nonmatching_alleles():
p1 = SimulatedProfile(fromfile=data_file("prof/red-strict-profile.json"))
p2 = SimulatedProfile(fromfile=data_file("prof/red-relaxed-profile.json"))
diff = list(mhapi.diff(p1, p2))
print(diff)
assert diff == [
("mh07CP-004", set(), {"T,T,T,A,T", "A,A,T,A,T"}),
("mh09KK-157", set(), {"G,C,C,A,T"}),
]
def main(args):
differ = mhapi.diff(Profile(fromfile=args.profile1),
Profile(fromfile=args.profile2))
with open(args.out, "w") as fh:
for marker, diff1, diff2 in differ:
print(marker, file=fh)
if len(diff1) > 0:
for haplotype in sorted(diff1):
print(">>>", haplotype, file=fh)
if len(diff2) > 0:
for haplotype in sorted(diff2):
print("<<<", haplotype, file=fh)
def test_diff_large():
gt1 = SimulatedProfile(fromfile=data_file("prof/diff-comp-1.json"))
gt2 = SimulatedProfile(fromfile=data_file("prof/diff-comp-3.json"))
diff = list(mhapi.diff(gt1, gt2))
loci = [d[0] for d in diff]
print(diff[9], diff[17], diff[21])
assert loci == [
"MHDBL000002",
"MHDBL000003",
"MHDBL000007",
"MHDBL000013",
"MHDBL000017",
"MHDBL000018",
"MHDBL000030",
"MHDBL000036",
"MHDBL000038",
"MHDBL000047",
"MHDBL000058",
"MHDBL000061",
"MHDBL000076",
"MHDBL000079",
"MHDBL000082",
"MHDBL000085",
"MHDBL000088",
"MHDBL000101",
"MHDBL000106",
"MHDBL000108",
"MHDBL000111",
"MHDBL000112",
"MHDBL000122",
"MHDBL000124",
"MHDBL000128",
"MHDBL000129",
"MHDBL000135",
"MHDBL000136",
"MHDBL000138",
"MHDBL000140",
"MHDBL000144",
"MHDBL000152",
"MHDBL000154",
"MHDBL000163",
"MHDBL000181",
"MHDBL000183",
"MHDBL000194",
"MHDBL000210",
"MHDBL000211",
"MHDBL000212",
]
assert diff[9] == ("MHDBL000047", set(), {"T,T"})
assert diff[17] == ("MHDBL000101", {"C,C,C,T"}, {"T,C,C,C"})
assert diff[21] == ("MHDBL000112", {"G,G,A,C"}, set())
def test_diff2():
gt1 = SimulatedProfile(fromfile=data_file("prof/euramer-sim-gt.json"))
gt2 = SimulatedProfile(fromfile=data_file("prof/euramer-inf-gt.json"))
diff = list(mhapi.diff(gt1, gt2))
assert diff == [("MHDBL000018", set(), {"T,G,C,T,A"})]