def test_blockcut_sensitivities(tmp_path):
""" Ensure that the block cut sets are monotone to the sensitivity"""
results = []
for s in range(6):
outvcf = tmp_path / "output{}.vcf".format(s)
run_polyphase(
phase_input_files=["tests/data/polyploid.chr22.42M.12k.bam"],
variant_file="tests/data/polyploid.chr22.42M.12k.vcf",
ploidy=4,
ignore_read_groups=True,
block_cut_sensitivity=s,
output=outvcf,
)
assert os.path.isfile(outvcf)
tables = list(VcfReader(outvcf, phases=True))
assert len(tables) == 1
block_starts = set([
i.block_id for i in tables[0].phases_of("HG00514_NA19240")
if i is not None
])
results.append(block_starts)
print(block_starts)
for s in range(5):
assert all(cut in results[s + 1] for cut in results[s])
def test_wrong_ploidy(tmp_path):
outvcf = tmp_path / "output.vcf"
with raises(CommandLineError):
run_polyphase(
phase_input_files=["tests/data/polyploid.chr22.42M.12k.bam"],
variant_file="tests/data/polyploid.chr22.42M.12k.vcf",
ploidy=3,
ignore_read_groups=True,
output=outvcf,
)
def test_polyphase_short_chr22(tmp_path):
outvcf = tmp_path / "output.vcf"
run_polyphase(
phase_input_files=["tests/data/polyploid.chr22.42M.12k.bam"],
variant_file="tests/data/polyploid.chr22.42M.12k.vcf",
ploidy=4,
ignore_read_groups=True,
output=outvcf,
)
assert os.path.isfile(outvcf)
tables = list(VcfReader(outvcf, phases=True))
assert len(tables) == 1
table = tables[0]
assert table.chromosome == "chr22"
assert len(table.variants) == 42
assert table.samples == ["HG00514_NA19240"]
def test_polyphase_multiple_bam(tmp_path):
outvcf = tmp_path / "output.vcf"
run_polyphase(
phase_input_files=[
"tests/data/polyploid.human1.chr22.42M.5k.bam",
"tests/data/polyploid.human2.chr22.42M.5k.bam",
],
variant_file="tests/data/polyploid.multisample.chr22.42M.5k.vcf",
ploidy=2,
ignore_read_groups=False,
output=outvcf,
)
assert os.path.isfile(outvcf)
tables = list(VcfReader(outvcf, phases=True))
assert len(tables) == 1
table = tables[0]
assert table.chromosome == "chr22"
assert len(table.variants) == 9
assert set(table.samples) == set(["HG00514", "NA19240"])
assert not all(p is None for p in table.phases_of("HG00514"))
assert not all(p is None for p in table.phases_of("NA19240"))
def test_polyphase_multithreaded(tmp_path):
outvcf_st = tmp_path / "output_st.vcf"
outvcf_mt = tmp_path / "output_mt.vcf"
run_polyphase(
phase_input_files=["tests/data/polyploid.chr22.42M.12k.bam"],
variant_file="tests/data/polyploid.chr22.42M.12k.vcf",
ploidy=4,
ignore_read_groups=True,
output=outvcf_st,
)
run_polyphase(
phase_input_files=["tests/data/polyploid.chr22.42M.12k.bam"],
variant_file="tests/data/polyploid.chr22.42M.12k.vcf",
ploidy=4,
ignore_read_groups=True,
output=outvcf_mt,
threads=4,
)
assert os.path.isfile(outvcf_st)
assert os.path.isfile(outvcf_mt)
tables_st = list(VcfReader(outvcf_st, phases=True))
table_st = tables_st[0]
tables_mt = list(VcfReader(outvcf_mt, phases=True))
table_mt = tables_mt[0]
assert table_st.chromosome == table_mt.chromosome
assert table_st.samples == table_mt.samples
assert all(
[st == mt for (st, mt) in zip(table_st.genotypes, table_mt.genotypes)])
assert all(
[st == mt for (st, mt) in zip(table_st.phases, table_mt.phases)])
assert all([
st == mt for (st, mt) in zip(table_st.genotype_likelihoods,
table_mt.genotype_likelihoods)
])
assert all(
[st == mt for (st, mt) in zip(table_st.variants, table_mt.variants)])