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fix pedigree parsing for missing parents -- need to preserve missing … #921

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Merged
merged 2 commits into from
Nov 6, 2024
Merged

fix pedigree parsing for missing parents -- need to preserve missing … #921

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fix pedigree parsing for missing parents -- need to preserve missing …
bpblanken Oct 8, 2024
e29cbb6
ruff
bpblanken Oct 8, 2024
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13 changes: 3 additions & 10 deletions v03_pipeline/lib/misc/pedigree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ def __hash__(self):
return hash(self.family_guid)

@staticmethod
def parse_direct_lineage(rows: list[hl.Struct]) -> dict[str, Sample]: # noqa: C901
def parse_direct_lineage(rows: list[hl.Struct]) -> dict[str, Sample]:
samples = {}
for row in rows:
samples[row.s] = Sample(
Expand All @@ -94,22 +94,15 @@ def parse_direct_lineage(rows: list[hl.Struct]) -> dict[str, Sample]: # noqa: C
for row in rows:
# Maternal GrandParents
maternal_s = samples[row.s].mother
if maternal_s and maternal_s not in samples:
# A sample id may be referenced for a proband that has been
# removed from the pedigree as an individual. We handle this by
# nulling out the parent here.
samples[row.s].mother = None
elif maternal_s:
if maternal_s and maternal_s in samples:
if samples[maternal_s].mother:
samples[row.s].maternal_grandmother = samples[maternal_s].mother
if samples[maternal_s].father:
samples[row.s].maternal_grandfather = samples[maternal_s].father

# Paternal GrandParents
paternal_s = samples[row.s].father
if paternal_s and paternal_s not in samples:
samples[row.s].father = None
elif paternal_s:
if paternal_s and paternal_s in samples:
if samples[paternal_s].mother:
samples[row.s].paternal_grandmother = samples[paternal_s].mother
if samples[paternal_s].father:
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8 changes: 7 additions & 1 deletion v03_pipeline/lib/misc/pedigree_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -479,7 +479,13 @@ def test_subsetted_pedigree_with_removed_parent(self) -> None:
),
)
self.assertEqual(len(family.samples), 2)
self.assertIsNone(family.samples['BBL_BC1-000345_01_D1'].father)
self.assertFalse(
'BBL_BC1-000345_02_D1' in family.samples,
)
self.assertEqual(
family.samples['BBL_BC1-000345_01_D1'].father,
'BBL_BC1-000345_02_D1',
)
self.assertEqual(
family.samples['BBL_BC1-000345_01_D1'].mother,
'BBL_BC1-000345_03_D1',
Expand Down
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