def test_compare1(tmp_path):
outtsv = tmp_path / "output.tsv"
run_compare(
vcf=["tests/data/phased1.vcf", "tests/data/phased2.vcf"],
ploidy=2,
names="p1,p2",
tsv_pairwise=outtsv,
sample="sample1",
)
lines = [l.split("\t") for l in open(outtsv)]
assert len(lines) == 3
Fields = namedtuple("Fields", [f.strip("#\n") for f in lines[0]])
entry_chrA, entry_chrB = [Fields(*l) for l in lines[1:]]
assert entry_chrA.chromosome == "chrA"
assert entry_chrA.all_assessed_pairs == "4"
assert entry_chrA.all_switches == "1"
assert entry_chrA.all_switchflips == "1/0"
assert entry_chrA.blockwise_hamming == "1"
assert entry_chrA.largestblock_assessed_pairs == "2"
assert entry_chrA.largestblock_switches == "1"
assert entry_chrA.largestblock_hamming == "1"
assert entry_chrB.chromosome == "chrB"
assert entry_chrB.all_assessed_pairs == "1"
assert entry_chrB.all_switches == "0"
assert entry_chrB.all_switchflips == "0/0"
assert entry_chrB.blockwise_hamming == "0"
assert entry_chrB.largestblock_assessed_pairs == "1"
assert entry_chrB.largestblock_switches == "0"
assert entry_chrB.largestblock_hamming == "0"
def test_compare_unphased():
run_compare(
vcf=[
"tests/data/unphased.vcf", "tests/data/unphased.vcf",
"tests/data/unphased.vcf"
],
ploidy=2,
sample="sample1",
)
def test_compare_polyploid2(tmp_path):
outtsv = tmp_path / "output.tsv"
run_compare(
vcf=["tests/data/phased.poly1.vcf", "tests/data/phased.poly2.vcf"],
ploidy=4,
names="p1,p2",
tsv_pairwise=outtsv,
sample="sample2",
)
with open(outtsv) as t:
lines = [line.split("\t") for line in t]
assert len(lines) == 3
Fields = namedtuple("Fields", [f.strip("#\n") for f in lines[0]])
entry_chr21, entry_chr22 = [Fields(*l) for l in lines[1:]]
assert entry_chr21.chromosome == "chr21"
assert entry_chr21.all_assessed_pairs == "3"
assert entry_chr21.all_switches == "0.5"
assert entry_chr21.all_switchflips in ["0.5/0.0", "0.0/0.5"]
assert entry_chr21.blockwise_hamming == "0.5"
assert entry_chr21.blockwise_diff_genotypes == "0"
assert entry_chr21.largestblock_assessed_pairs == "3"
assert entry_chr21.largestblock_switches == "0.5"
assert entry_chr21.largestblock_switchflips in ["0.5/0.0", "0.0/0.5"]
assert entry_chr21.largestblock_hamming == "0.5"
assert entry_chr21.largestblock_diff_genotypes == "0"
assert entry_chr22.chromosome == "chr22"
assert entry_chr22.all_assessed_pairs == "5"
assert entry_chr22.all_switches == "1.0"
assert entry_chr22.all_switchflips in ["1.0/0.0", "0.5/0.5", "0.0/1.0"]
assert entry_chr22.blockwise_hamming == "1.0"
assert entry_chr22.blockwise_diff_genotypes == "0"
assert entry_chr22.largestblock_assessed_pairs == "3"
assert entry_chr22.largestblock_switches == "0.5"
assert entry_chr22.largestblock_switchflips in ["0.5/0.0", "0.0/0.5"]
assert entry_chr22.largestblock_hamming == "0.5"
assert entry_chr22.largestblock_diff_genotypes == "0"
