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feat: Handle parsing empty predicted sex into Unknown (#1000)
1 parent 533d1d4 commit b98fe66

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4 files changed

+12
-6
lines changed

4 files changed

+12
-6
lines changed

‎v03_pipeline/lib/misc/io.py

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -219,7 +219,11 @@ def select_relevant_fields(
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def import_imputed_sex(imputed_sex_path: str) -> hl.Table:
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ht = hl.import_table(imputed_sex_path)
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imputed_sex_lookup = hl.dict(
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{s.imputed_sex_value: s.value for s in Sex},
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{
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imputed_sex_value: s.value
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for s in Sex
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for imputed_sex_value in s.imputed_sex_values
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},
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)
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ht = ht.select(
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s=ht.collaborator_sample_id,

‎v03_pipeline/lib/misc/io_test.py

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Original file line numberDiff line numberDiff line change
@@ -47,6 +47,7 @@ def test_import_imputed_sex(self) -> None:
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hl.Struct(s='abc_2', predicted_sex='F'),
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hl.Struct(s='abc_3', predicted_sex='U'),
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hl.Struct(s='abc_4', predicted_sex='XYY'),
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hl.Struct(s='abc_5', predicted_sex='U'),
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],
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)
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‎v03_pipeline/lib/model/definitions.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -18,12 +18,12 @@ class Sex(str, Enum):
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XYY = 'XYY'
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@property
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def imputed_sex_value(self):
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def imputed_sex_values(self) -> list[str]:
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return {
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Sex.MALE: 'Male',
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Sex.FEMALE: 'Female',
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Sex.UNKNOWN: 'Unknown',
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}.get(self, self.name)
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Sex.MALE: ['Male'],
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Sex.FEMALE: ['Female'],
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Sex.UNKNOWN: ['', 'Unknown'],
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}.get(self, [self.name])
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class PipelineVersion(str, Enum):

‎v03_pipeline/var/test/sex_check/test_imputed_sex.tsv

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