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add tests for ResultRanker class
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@yaseminbridges
yaseminbridges committed Nov 5, 2024
1 parent 2941463 commit 1c12523
Showing 1 changed file with 156 additions and 35 deletions.
191 changes: 156 additions & 35 deletions tests/test_post_processing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,10 @@
RankedPhEvalDiseaseResult,
RankedPhEvalGeneResult,
RankedPhEvalVariantResult,
ResultRanker,
ResultSorter,
SortOrder,
_create_pheval_result,
_rank_pheval_result,
_return_sort_order,
calculate_end_pos,
)
Expand Down Expand Up @@ -217,41 +217,145 @@ def test_sort_pheval_results_pvalue(self):
)


class TestRankPhEvalResults(unittest.TestCase):
class TestResultRanker(unittest.TestCase):
@classmethod
def setUpClass(cls) -> None:
cls.sorted_gene_result = [
PhEvalGeneResult(
gene_symbol="MAP3K14", gene_identifier="ENSG00000006062", score=0.9234
),
PhEvalGeneResult(gene_symbol="A4GNT", gene_identifier="ENSG00000118017", score=0.6529),
PhEvalGeneResult(gene_symbol="OR14J1", gene_identifier="ENSG00000204695", score=0.6529),
PhEvalGeneResult(gene_symbol="PAGE1", gene_identifier="ENSG00000068985", score=0.5235),
]
cls.sorted_variant_result = [
PhEvalVariantResult(
chromosome="X", start=93473023, end=93473024, ref="A", alt="G", score=0.1245
),
PhEvalVariantResult(
chromosome="8", start=532356, end=532357, ref="A", alt="C", score=0.4578
),
PhEvalVariantResult(
chromosome="5",
start=23457444233,
end=23457444234,
ref="A",
alt="C",
score=0.9348,
),
PhEvalVariantResult(
chromosome="12", start=12754332, end=12754333, ref="T", alt="G", score=0.9999
),
]
cls.sorted_disease_result = pheval_disease_result
cls.gene_result_ranker = ResultRanker(
[
PhEvalGeneResult(
gene_symbol="MAP3K14", gene_identifier="ENSG00000006062", score=0.9234
),
PhEvalGeneResult(
gene_symbol="A4GNT", gene_identifier="ENSG00000118017", score=0.6529
),
PhEvalGeneResult(
gene_symbol="OR14J1", gene_identifier="ENSG00000204695", score=0.6529
),
PhEvalGeneResult(
gene_symbol="PAGE1", gene_identifier="ENSG00000068985", score=0.5235
),
],
SortOrder.DESCENDING,
)
cls.variant_result_ranker = ResultRanker(
[
PhEvalVariantResult(
chromosome="X", start=93473023, end=93473024, ref="A", alt="G", score=0.1245
),
PhEvalVariantResult(
chromosome="8", start=532356, end=532357, ref="A", alt="C", score=0.4578
),
PhEvalVariantResult(
chromosome="5",
start=23457444233,
end=23457444234,
ref="A",
alt="C",
score=0.9999,
),
PhEvalVariantResult(
chromosome="12", start=12754332, end=12754333, ref="T", alt="G", score=0.9999
),
],
sort_order=SortOrder.ASCENDING,
)
cls.variant_result_ranker_grouping_id = ResultRanker(
[
PhEvalVariantResult(
chromosome="X",
start=93473023,
end=93473024,
ref="A",
alt="G",
score=0.1245,
grouping_id="4567",
),
PhEvalVariantResult(
chromosome="8",
start=532356,
end=532357,
ref="A",
alt="C",
score=0.4578,
grouping_id="789",
),
PhEvalVariantResult(
chromosome="5",
start=23457444233,
end=23457444234,
ref="A",
alt="C",
score=0.9999,
grouping_id="12345",
),
PhEvalVariantResult(
chromosome="12",
start=12754332,
end=12754333,
ref="T",
alt="G",
score=0.9999,
grouping_id="12345",
),
],
sort_order=SortOrder.DESCENDING,
)
cls.disease_result_ranker = ResultRanker(
pheval_disease_result, sort_order=SortOrder.DESCENDING
)

def test__has_valid_grouping_id(self):
df = pd.DataFrame({"score": [0.5, 0.7, 0.3], "grouping_id": ["A", "B", "C"]})
self.assertTrue(self.variant_result_ranker._has_valid_grouping_id(df))

def test__has_valid_grouping_id_present_with_none(self):
df = pd.DataFrame({"score": [0.5, 0.7, 0.3], "grouping_id": ["A", None, "C"]})
self.assertFalse(self.variant_result_ranker._has_valid_grouping_id(df))

def test__has_valid_grouping_id_not_present(self):
df = pd.DataFrame({"score": [0.5, 0.7, 0.3]})
self.assertFalse(self.variant_result_ranker._has_valid_grouping_id(df))

def test__rank_with_grouping_id(self):
df = pd.DataFrame(
{
"score": [0.9, 0.9, 0.8, 0.7, 0.7, 0.6, 0.5, 0.5, 0.4],
"grouping_id": ["A", "A", "B", "C", "D", "E", "F", "F", "G"],
}
)
self.assertTrue(
self.gene_result_ranker._rank_with_grouping_id(df).equals(
pd.DataFrame(
{
"score": [0.9, 0.9, 0.8, 0.7, 0.7, 0.6, 0.5, 0.5, 0.4],
"grouping_id": ["A", "A", "B", "C", "D", "E", "F", "F", "G"],
"min_rank": [1.0, 1.0, 3.0, 5.0, 4.0, 6.0, 7.0, 7.0, 9.0],
"rank": [1.0, 1.0, 3.0, 5.0, 5.0, 6.0, 7.0, 7.0, 9.0],
}
)
)
)

def test__rank_without_grouping_id(self):
df = pd.DataFrame(
{
"score": [0.9, 0.9, 0.8, 0.7, 0.7, 0.6, 0.5, 0.5, 0.4],
}
)
self.assertTrue(
self.gene_result_ranker._rank_without_grouping_id(df).equals(
pd.DataFrame(
{
"score": [0.9, 0.9, 0.8, 0.7, 0.7, 0.6, 0.5, 0.5, 0.4],
"rank": [2.0, 2.0, 3.0, 5.0, 5.0, 6.0, 8.0, 8.0, 9.0],
}
)
)
)

def test_rank_pheval_results_gene(self):
self.assertTrue(
_rank_pheval_result(self.sorted_gene_result, SortOrder.DESCENDING).equals(
self.gene_result_ranker.rank().equals(
pd.DataFrame(
{
"gene_symbol": ["MAP3K14", "A4GNT", "OR14J1", "PAGE1"],
Expand All @@ -270,24 +374,41 @@ def test_rank_pheval_results_gene(self):

def test_rank_pheval_results_variant(self):
self.assertTrue(
_rank_pheval_result(self.sorted_variant_result, SortOrder.ASCENDING).equals(
self.variant_result_ranker.rank().equals(
pd.DataFrame(
{
"chromosome": ["X", "8", "5", "12"],
"start": [93473023, 532356, 23457444233, 12754332],
"end": [93473024, 532357, 23457444234, 12754333],
"ref": ["A", "A", "A", "T"],
"alt": ["G", "C", "C", "G"],
"score": [0.1245, 0.4578, 0.9348, 0.9999],
"rank": [1.0, 2.0, 3.0, 4.0],
"score": [0.1245, 0.4578, 0.9999, 0.9999],
"rank": [1.0, 2.0, 4.0, 4.0],
}
)
)
)

def test_rank_pheval_results_variant_grouping_id(self):
self.assertTrue(
self.variant_result_ranker_grouping_id.rank().equals(
pd.DataFrame(
{
"chromosome": ["X", "8", "5", "12"],
"start": [93473023, 532356, 23457444233, 12754332],
"end": [93473024, 532357, 23457444234, 12754333],
"ref": ["A", "A", "A", "T"],
"alt": ["G", "C", "C", "G"],
"score": [0.1245, 0.4578, 0.9999, 0.9999],
"rank": [4.0, 3.0, 1.0, 1.0],
}
)
)
)

def test_rank_pheval_results_disease(self):
self.assertTrue(
_rank_pheval_result(self.sorted_disease_result, SortOrder.DESCENDING).equals(
self.disease_result_ranker.rank().equals(
pd.DataFrame(
{
"disease_name": {
Expand Down

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