def create_test_snpit():
positions = [2, 5, 8, 11, 14, 16, 20]
names = [
[("L1", "A")],
[("L2", "C")],
[("L1", "A"), ("L4", "C")],
[("L2", "T"), ("L3", "G")],
[("L3", "A")],
[("L4", "G")],
[("L1", "C"), ("L3", "T"), ("L4", "G")],
]
lineages = {
"L1": Lineage(name="L1", species="S1", lineage="Lin1", sublineage="SL1"),
"L2": Lineage(name="L2", species="S2", lineage="Lin2", sublineage="SL2"),
"L3": Lineage(name="L3", species="S3", lineage="Lin3", sublineage="SL3"),
"L4": Lineage(name="L4", species="S4", lineage="Lineage 4", sublineage="SL4"),
}
position_map = dict()
for i in range(len(positions)):
position_map[positions[i]] = {}
for name, variant in names[i]:
if variant not in position_map[positions[i]]:
position_map[positions[i]][variant] = [name]
else:
position_map[positions[i]][variant].append(name)
snpit = SnpIt(threshold=10)
snpit.lineages = lineages
snpit.lineage_positions = position_map
return snpit
def test_fromCsvEntry_emptyEntryReturnsEmptyLineage():
entry = dict()
actual = Lineage.from_csv_entry(entry)
expected = Lineage()
assert actual == expected
def test_addSnps_emptyFileSnpsRemainEmpty():
lineage_variant_file = TEST_CASE_DIR / "empty.tsv"
lineage = Lineage()
lineage.add_snps(lineage_variant_file)
actual = lineage.snps
expected = dict()
assert actual == expected
def test_fromCsvEntry_realEntryEntryReturnsLineage():
library = csv.DictReader(TEST_CASE_DIR.joinpath("test_library.csv").open())
entry = next(library)
actual = Lineage.from_csv_entry(entry)
expected = Lineage(
species="M. tuberculosis",
lineage="Lineage 1",
sublineage="Sublineage 7",
name="Indo_Oceanic",
)
assert actual == expected
def test_addSnps_realFileSnpsContainAllEntries():
lineage_variant_file = TEST_CASE_DIR / "test_lineage.tsv"
lineage = Lineage()
lineage.add_snps(lineage_variant_file)
actual = lineage.snps
expected = {
1011511: "C",
1022003: "C",
1028217: "A",
1034758: "T",
1071966: "G"
}
assert actual == expected
def test_classifyFasta_multiSampleFastaReturnMultiSample():
fasta_path = TEST_CASE_DIR / "multi_sample.fa"
snpit = create_test_snpit()
snpit.lineages["L1"].snps = {x: "A" for x in range(10)}
snpit.lineages["L2"].snps = {x: "A" for x in range(20)}
snpit.lineages["L3"].snps = {x: "A" for x in range(20)}
snpit.lineages["L4"].snps = {x: "A" for x in range(2)}
actual = snpit.classify_fasta(fasta_path)
expected = {
"Sample1": (50.0, Lineage(name="L4")),
"Sample2": (20.0, Lineage(name="L1")),
}
assert actual == expected
def test_outputResults_twoSamplesResultsWritesTwoSamples():
outfile = StringIO()
results = {
"Sample1": (25.2533333, Lineage(name="L1", sublineage="SL1")),
"Sample2": (75.75899, Lineage(name="L2", species="S2", lineage="Lin2")),
}
output_results(outfile, results)
outfile.seek(0)
actual = outfile.read()
expected = (
"Sample\tSpecies\tLineage\tSublineage\tName\tPercentage\n"
"Sample1\tN/A\tN/A\tSL1\tL1\t25.25\n"
"Sample2\tS2\tLin2\tN/A\tL2\t75.76\n"
)
assert actual == expected
def test_determineLineage_emptyCountsInReturnsEmptyResults():
snpit = create_test_snpit()
snpit.lineages = {}
actual_percentage, actual_lineage = snpit.determine_lineage(Counter())
expected_percentage, expected_lineage = (0, Lineage())
assert actual_percentage == expected_percentage
assert actual_lineage == actual_lineage
def test_loadLineagesFromCsv_fileWithTwoEntriesReturnsDictWithTwoLineages():
filepath = TEST_CASE_DIR / "test_library.csv"
beijing_lineage = Lineage(
name="beijing", species="M. tuberculosis", lineage="Lineage 2", sublineage=""
)
indo_lineage = Lineage(
name="Indo_Oceanic",
species="M. tuberculosis",
lineage="Lineage 1",
sublineage="Sublineage 7",
)
actual_lineages, actual_position_map = load_lineages_from_csv(filepath)
assert len(actual_position_map) == 714
assert actual_position_map[1083755] == {"G": [indo_lineage.name]}
assert actual_position_map[1288698] == {"A": [beijing_lineage.name]}
assert actual_lineages["beijing"] == beijing_lineage
assert actual_lineages["Indo_Oceanic"] == indo_lineage
def test_outputResults_emptySampleResultsWritesSampleWithNAs():
outfile = StringIO()
results = dict(Sample1=(0, Lineage()))
output_results(outfile, results)
outfile.seek(0)
actual = outfile.read()
expected = (
"Sample\tSpecies\tLineage\tSublineage\tName\tPercentage\n"
"Sample1\tN/A\tN/A\tN/A\tN/A\t0\n"
)
assert actual == expected
def test_classifyVcf_exampleVcfReturnsCorrectClassification():
snpit = SnpIt(10, True)
vcf_path = TEST_CASE_DIR / "example.vcf"
actual = snpit.classify_vcf(vcf_path)
expected = {
"example": (
97.2972972972973,
Lineage(lineage="Lineage 2", species="M. tuberculosis", name="beijing"),
)
}
assert actual == expected
def test_determineLineage_L4MostCountsReturnsL4():
snpit = create_test_snpit()
dummy_snps = {x: "A" for x in range(10)}
snpit.lineages["L4"].snps = dummy_snps
snpit.lineages["L1"].snps = dummy_snps
actual_percentage, actual_lineage = snpit.determine_lineage(
Counter(["L4", "L1", "L4"])
)
expected_percentage, expected_lineage = (
20.0,
Lineage(name="L4", species="S3", lineage="Lin3", sublineage="SL3"),
)
assert actual_percentage == expected_percentage
assert actual_lineage == actual_lineage
def test_determineLineage_L4NoSublineageMostCountsNextBestL4WithSublineageReturnsNextBest():
snpit = create_test_snpit()
dummy_snps = {x: "A" for x in range(10)}
snpit.lineages["L4"].snps = dummy_snps
snpit.lineages["L1"].snps = dummy_snps
snpit.lineages["L4"].sublineage = ""
snpit.lineages["L1"].lineage = "Lineage 4"
snpit.lineages["L1"].sublineage = "corner case"
actual_percentage, actual_lineage = snpit.determine_lineage(
Counter(["L4", "L1", "L4"])
)
expected_percentage, expected_lineage = (
20.0,
Lineage(name="L1", species="S1", lineage="Lineage 4", sublineage="corner case"),
)
assert actual_percentage == expected_percentage
assert actual_lineage == actual_lineage
def test_inequalityOperator_twoNonEqualReturnsTrue():
lineage1 = Lineage(name="foo", lineage="Lineage 5")
lineage2 = Lineage(name="test", lineage="Lineage 6")
assert lineage1 != lineage2
def test_lessThanOperator_xEqualsYReturnsFalse():
x = Lineage(name="bar")
y = Lineage(name="bar")
assert not (x < y)
def test_inequalityOperator_twoEqualReturnsFalse():
lineage1 = Lineage(name="test", lineage="Lineage 5")
lineage2 = Lineage(name="test", lineage="Lineage 6")
assert not (lineage1 != lineage2)
def test_greaterThanOperator_xLessThanYReturnsFalse():
x = Lineage(name="bar")
y = Lineage(name="foo")
assert not (x > y)
def test_lessThanOperator_xLessThanYReturnsTrue():
x = Lineage(name="bar")
y = Lineage(name="foo")
assert x < y
def test_greaterThanOperator_xGreaterThanYReturnsTrue():
x = Lineage(name="foo")
y = Lineage(name="bar")
assert x > y
def test_equalityOperator_twoEqualReturnsTrue():
lineage1 = Lineage(name="test", lineage="Lineage 5")
lineage2 = Lineage(name="test", lineage="Lineage 6")
assert lineage1 == lineage2
def test_greaterThanOperator_xEqualsYReturnsFalse():
x = Lineage(name="bar")
y = Lineage(name="bar")
assert not (x > y)