def test_type_filter_threshold():
bam = data_file("bam/dyncut-test-reads.bam")
tsv = data_file("def/dyncut-panel.tsv")
rslt = mhapi.type(bam, tsv)
rslt.filter(static=10, dynamic=0.005)
assert rslt.haplotypes("MHDBL000018") == set(["C,A,C,T,G", "T,G,C,T,G"])
assert rslt.haplotypes("MHDBL000156") == set(["T,C,A,C", "T,C,G,G"])
rslt = mhapi.type(bam, tsv)
rslt.filter(static=4, dynamic=0.005)
assert rslt.haplotypes("MHDBL000018") == set(
["C,A,C,T,G", "T,G,C,T,G", "C,A,C,T,A", "T,G,C,T,A"])
assert rslt.haplotypes("MHDBL000156") == set(["T,C,A,C", "T,C,G,G"])
def test_filter_simple():
bam = data_file("pashtun-sim/aligned-reads.bam")
tsv = data_file("pashtun-sim/tiny-panel.tsv")
observed = mhapi.type(bam, tsv)
observed.filter(static=10, dynamic=0.05)
expected = TypingResult(fromfile=data_file("pashtun-sim/test-output.json"))
assert observed == expected
def test_type_simple():
bam = data_file("pashtun-sim/aligned-reads.bam")
tsv = data_file("pashtun-sim/tiny-panel.tsv")
result = mhapi.type(bam, tsv)
assert result.haplotypes("mh13KK-218") == set()
assert result.data["markers"]["mh13KK-218"]["typing_result"] == {
"C,T,C,G": 1,
"C,T,T,T": 1,
"G,T,C,T": 1,
"T,A,C,T": 1,
"T,G,C,T": 3,
"T,G,T,T": 2,
"T,T,A,T": 5,
"T,T,C,A": 1,
"T,T,C,C": 2,
"T,T,C,G": 2,
"T,T,C,T": 1178,
"T,T,G,T": 2,
"T,T,T,A": 2,
"T,T,T,G": 6,
"T,T,T,T": 1170,
}
assert result.haplotypes("mh21KK-320") == set()
assert result.data["markers"]["mh21KK-320"]["typing_result"] == {
"G,A,A,A": 1,
"G,A,C,A": 3,
"G,A,G,A": 3,
"G,A,T,A": 1075,
"G,A,T,C": 1,
"G,A,T,G": 1,
"G,A,T,T": 2,
"G,C,C,A": 1,
"G,C,T,A": 4,
"G,G,A,A": 2,
"G,G,A,T": 1,
"G,G,C,A": 1075,
"G,G,C,C": 3,
"G,G,C,G": 12,
"G,G,C,T": 5,
"G,G,T,A": 4,
"G,T,C,A": 1,
"T,G,C,A": 1,
}
def test_type_missing_bam_index(tmp_path):
bam = data_file("bam/three-contrib-log-link.bam")
tsv = data_file("def/default-panel-offsets.tsv")
tmp_bam = str(tmp_path / "reads.bam")
tmp_tsv = str(tmp_path / "offsets.tsv")
copyfile(bam, tmp_bam)
copyfile(tsv, tmp_tsv)
result = mhapi.type(tmp_bam, tmp_tsv, minbasequal=13)
ac30 = result.data["markers"]["MHDBL000030"]["typing_result"]
ac197 = result.data["markers"]["MHDBL000197"]["typing_result"]
assert ac30 == {
"A,A,T,C": 3,
"A,C,C,C": 2,
"A,C,C,G": 18,
"G,C,C,C": 1,
"G,C,C,G": 34
}
assert ac197 == {
"A,A,T,T,T": 30,
"A,A,T,T,C": 39,
"A,A,T,A,T": 1,
"A,A,T,A,C": 1
}
def test_type_marker_with_no_coverage():
bam = data_file("bam/nocov.bam")
tsv = data_file("def/nocov-offsets.tsv")
result = mhapi.type(bam, tsv)
for marker, mdata in result.data["markers"].items():
assert "genotype" in mdata
def test_type_no_var_offsets():
bam = data_file("bam/sandawe-dad.bam")
tsv = data_file("def/sandawe-empty.tsv")
message = r"marker IDs unique to set1={mh01KK-205, mh02KK-005, mh03KK-006};"
with pytest.raises(ValueError, match=message):
mhapi.type(bam, tsv)