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Will-Tylerjeromekelleher
Will-Tyler
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jeromekelleher
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Remove saved expected result
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2 files changed

+75
-7
lines changed

2 files changed

+75
-7
lines changed

‎tests/data/numpy/expected_call_LPL.npy‎

-8.21 KB
Binary file not shown.

‎tests/test_vcf_examples.py‎

Lines changed: 75 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -515,18 +515,13 @@ def test_ok_without_local_alleles(self, ds):
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516516
class Test1000G2020Example:
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data_path = "tests/data/vcf/1kg_2020_chrM.vcf.gz"
518-
expected_call_lpl_path = "tests/data/numpy/expected_call_LPL.npy"
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520519
@pytest.fixture(scope="class")
521520
def ds(self, tmp_path_factory):
522521
out = tmp_path_factory.mktemp("data") / "example.vcf.zarr"
523522
vcf2zarr.convert([self.data_path], out, worker_processes=0)
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return sg.load_dataset(out)
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526-
@pytest.fixture(scope="class")
527-
def expected_call_lpl(self):
528-
return np.load(self.expected_call_lpl_path)
529-
530525
def test_position(self, ds):
531526
# fmt: off
532527
pos = [
@@ -651,8 +646,81 @@ def test_call_LAA(self, ds):
651646
]
652647
nt.assert_array_equal(ds.call_LAA.values, call_LAA)
653648

654-
def test_call_LPL(self, ds, expected_call_lpl):
655-
nt.assert_array_equal(ds.call_LPL.values, expected_call_lpl)
649+
def test_call_LPL(self, ds):
650+
# fmt: off
651+
call_LPL = [
652+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
653+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
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[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
655+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
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[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
657+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
658+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
659+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
660+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
661+
[[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
662+
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
663+
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
664+
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
665+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
666+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]], # noqa: E501
667+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
668+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
669+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
670+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
671+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
672+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
673+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
674+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
675+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
676+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
677+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
678+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
679+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
680+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
681+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
682+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
683+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
684+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
685+
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
686+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
687+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]], # noqa: E501
688+
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
689+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
690+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]], # noqa: E501
691+
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
692+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
693+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]], # noqa: E501
694+
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
695+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
696+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]], # noqa: E501
697+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
698+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
699+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
700+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
701+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
702+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
703+
[[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
704+
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
705+
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
706+
[[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
707+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
708+
[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
709+
[[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
710+
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
711+
[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
712+
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
713+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
714+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]], # noqa: E501
715+
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
716+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800], # noqa: E501
717+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]], # noqa: E501
718+
[[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
719+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
720+
[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]]
721+
]
722+
# fmt: on
723+
nt.assert_array_equal(ds.call_LPL.values, call_LPL)
656724

657725
def test_call_PID(self, ds):
658726
call_PGT = ds["call_PGT"].values

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