def test_display_genotypes__duplicate_variant_ids():
ds = simulate_genotype_call_dataset(n_variant=3, n_sample=3, seed=0)
# set some variant IDs
ds["variant_id"] = (["variants"], np.array(["V0", "V1", "V1"]))
ds["variant_id_mask"] = (["variants"], np.array([False, False, False]))
disp = display_genotypes(ds)
expected = """\
samples S0 S1 S2
variants
0 0/0 1/0 1/0
1 0/1 1/0 0/1
2 0/0 1/0 1/1""" # noqa: W291
assert str(disp) == dedent(expected)
def test_display_genotypes__truncated_rows():
ds = simulate_genotype_call_dataset(n_variant=10, n_sample=10, seed=0)
disp = display_genotypes(ds, max_variants=4, max_samples=10)
expected = """\
samples S0 S1 S2 S3 S4 S5 S6 S7 S8 S9
variants
0 0/0 1/0 1/0 0/1 1/0 0/1 0/0 1/0 1/1 0/0
1 1/0 0/1 1/0 1/1 1/1 1/0 1/0 0/0 1/0 1/1
... ... ... ... ... ... ... ... ... ... ...
8 0/1 0/0 1/0 0/1 0/1 1/0 1/0 0/1 1/0 1/0
9 1/1 0/1 1/0 0/1 1/0 1/1 0/1 1/0 1/1 1/0
[10 rows x 10 columns]""" # noqa: W291
assert str(disp) == dedent(expected)
def test_display_genotypes():
ds = simulate_genotype_call_dataset(n_variant=3, n_sample=3, seed=0)
disp = display_genotypes(ds)
expected = """\
samples S0 S1 S2
variants
0 0/0 1/0 1/0
1 0/1 1/0 0/1
2 0/0 1/0 1/1""" # noqa: W291
assert str(disp) == dedent(expected)
expected_html = """<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th>samples</th>
<th>S0</th>
<th>S1</th>
<th>S2</th>
</tr>
<tr>
<th>variants</th>
<th></th>
<th></th>
<th></th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>0/0</td>
<td>1/0</td>
<td>1/0</td>
</tr>
<tr>
<th>1</th>
<td>0/1</td>
<td>1/0</td>
<td>0/1</td>
</tr>
<tr>
<th>2</th>
<td>0/0</td>
<td>1/0</td>
<td>1/1</td>
</tr>
</tbody>
</table>""".strip()
assert expected_html in disp._repr_html_()
def test_display_genotypes__large():
ds = simulate_genotype_call_dataset(n_variant=100_000,
n_sample=1000,
seed=0)
disp = display_genotypes(ds, max_variants=4, max_samples=4)
expected = """\
samples S0 S1 ... S998 S999
variants ...
0 0/0 1/0 ... 0/1 1/1
1 1/1 1/1 ... 0/1 1/1
... ... ... ... ... ...
99998 0/1 1/1 ... 1/0 0/1
99999 1/0 1/0 ... 1/0 1/0
[100000 rows x 1000 columns]""" # noqa: W291
assert str(disp) == dedent(expected)
def test_create_genotype_call_dataset():
variant_contig_names = ["chr1"]
variant_contig = np.array([0, 0], dtype="i1")
variant_position = np.array([1000, 2000], dtype="i4")
variant_allele = np.array([["A", "C"], ["G", "A"]], dtype="S1")
variant_id = np.array(["rs1", "rs2"], dtype=str)
sample_id = np.array(["sample_1", "sample_2", "sample_3"], dtype=str)
call_genotype = np.array(
[[[0, 0], [0, 1], [1, 0]], [[-1, 0], [0, -1], [-1, -1]]], dtype="i1")
call_genotype_phased = np.array(
[[True, True, False], [True, False, False]], dtype=bool)
ds = create_genotype_call_dataset(
variant_contig_names=variant_contig_names,
variant_contig=variant_contig,
variant_position=variant_position,
variant_allele=variant_allele,
sample_id=sample_id,
call_genotype=call_genotype,
call_genotype_phased=call_genotype_phased,
variant_id=variant_id,
)
assert DIM_VARIANT in ds.dims
assert DIM_SAMPLE in ds.dims
assert DIM_PLOIDY in ds.dims
assert DIM_ALLELE in ds.dims
assert ds.attrs["source"] == f"sgkit-{__version__}"
assert ds.attrs["contigs"] == variant_contig_names
assert_array_equal(ds["variant_contig"], variant_contig)
assert_array_equal(ds["variant_position"], variant_position)
assert_array_equal(ds["variant_allele"], variant_allele)
assert_array_equal(ds["variant_id"], variant_id)
assert_array_equal(ds["sample_id"], sample_id)
assert_array_equal(ds["call_genotype"], call_genotype)
assert_array_equal(ds["call_genotype_mask"], call_genotype < 0)
assert_array_equal(ds["call_genotype_phased"], call_genotype_phased)
disp = display_genotypes(ds)
assert (str(disp) == """
samples sample_1 sample_2 sample_3
variants
rs1 0|0 0|1 1/0
rs2 .|0 0/. ./.
""".strip() # noqa: W291
)
def test_display_genotypes__truncated_columns():
ds = simulate_genotype_call_dataset(n_variant=10, n_sample=10, seed=0)
disp = display_genotypes(ds, max_variants=10, max_samples=4)
expected = """\
samples S0 S1 ... S8 S9
variants ...
0 0/0 1/0 ... 1/1 0/0
1 1/0 0/1 ... 1/0 1/1
2 1/1 1/1 ... 0/0 1/0
3 0/1 0/0 ... 1/0 0/0
4 0/1 0/0 ... 0/0 1/1
5 1/1 1/0 ... 0/0 1/0
6 1/1 0/0 ... 1/0 0/1
7 1/0 0/1 ... 0/1 0/0
8 0/1 0/0 ... 1/0 1/0
9 1/1 0/1 ... 1/1 1/0
[10 rows x 10 columns]""" # noqa: W291
assert str(disp) == dedent(expected)
def test_display_genotypes__truncated_rows_and_columns():
ds = simulate_genotype_call_dataset(n_variant=10, n_sample=10, seed=0)
disp = display_genotypes(ds, max_variants=4, max_samples=4)
expected = """\
samples S0 S1 ... S8 S9
variants ...
0 0/0 1/0 ... 1/1 0/0
1 1/0 0/1 ... 1/0 1/1
... ... ... ... ... ...
8 0/1 0/0 ... 1/0 1/0
9 1/1 0/1 ... 1/1 1/0
[10 rows x 10 columns]""" # noqa: W291
assert str(disp) == dedent(expected)
expected_html = """<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th>samples</th>
<th>S0</th>
<th>S1</th>
<th>...</th>
<th>S8</th>
<th>S9</th>
</tr>
<tr>
<th>variants</th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>0/0</td>
<td>1/0</td>
<td>...</td>
<td>1/1</td>
<td>0/0</td>
</tr>
<tr>
<th>1</th>
<td>1/0</td>
<td>0/1</td>
<td>...</td>
<td>1/0</td>
<td>1/1</td>
</tr>
<tr>
<th>...</th>
<td>...</td>
<td>...</td>
<td>...</td>
<td>...</td>
<td>...</td>
</tr>
<tr>
<th>8</th>
<td>0/1</td>
<td>0/0</td>
<td>...</td>
<td>1/0</td>
<td>1/0</td>
</tr>
<tr>
<th>9</th>
<td>1/1</td>
<td>0/1</td>
<td>...</td>
<td>1/1</td>
<td>1/0</td>
</tr>
</tbody>
</table>
<p>10 rows x 10 columns</p>""".strip()
assert expected_html in disp._repr_html_()