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feat: Handle parsing empty predicted sex into Unknown #1000

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Merged
merged 1 commit into from
Dec 13, 2024
Merged

feat: Handle parsing empty predicted sex into Unknown #1000

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6 changes: 5 additions & 1 deletion v03_pipeline/lib/misc/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,11 @@ def select_relevant_fields(
def import_imputed_sex(imputed_sex_path: str) -> hl.Table:
ht = hl.import_table(imputed_sex_path)
imputed_sex_lookup = hl.dict(
{s.imputed_sex_value: s.value for s in Sex},
{
imputed_sex_value: s.value
for s in Sex
for imputed_sex_value in s.imputed_sex_values
},
)
ht = ht.select(
s=ht.collaborator_sample_id,
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1 change: 1 addition & 0 deletions v03_pipeline/lib/misc/io_test.py
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Expand Up @@ -47,6 +47,7 @@ def test_import_imputed_sex(self) -> None:
hl.Struct(s='abc_2', predicted_sex='F'),
hl.Struct(s='abc_3', predicted_sex='U'),
hl.Struct(s='abc_4', predicted_sex='XYY'),
hl.Struct(s='abc_5', predicted_sex='U'),
],
)

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10 changes: 5 additions & 5 deletions v03_pipeline/lib/model/definitions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,12 @@ class Sex(str, Enum):
XYY = 'XYY'

@property
def imputed_sex_value(self):
def imputed_sex_values(self) -> list[str]:
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Collaborator Author

@bpblanken bpblanken Dec 13, 2024 •
edited
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todo: this should be renamed to predicted_sex value but it was too messy to handle on this pr.

return {
Sex.MALE: 'Male',
Sex.FEMALE: 'Female',
Sex.UNKNOWN: 'Unknown',
}.get(self, self.name)
Sex.MALE: ['Male'],
Sex.FEMALE: ['Female'],
Sex.UNKNOWN: ['', 'Unknown'],
}.get(self, [self.name])


class PipelineVersion(str, Enum):
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1 change: 1 addition & 0 deletions v03_pipeline/var/test/sex_check/test_imputed_sex.tsv
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Original file line number Diff line number Diff line change
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