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Fix to only add the error_rate annotation if fit is not supplied to assign_population_pcs #453

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Merged
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May 20, 2022
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Fix to only add the error_rate annotation if fit is not supplied to assign_population_pcs #453

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20 changes: 13 additions & 7 deletions gnomad/sample_qc/ancestry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -237,14 +237,20 @@ def assign_population_pcs(
if hail_input:
pops_ht = hl.Table.from_pandas(pop_pc_pd, key=list(pop_pca_scores.key))
pops_ht = pops_ht.annotate_globals(
assign_pops_from_pc_params=hl.struct(
min_assignment_prob=min_prob, error_rate=error_rate
)
)
pops_ht = pops_ht.annotate(
evaluation_sample=hl.literal(list(evaluate_fit.s)).contains(pops_ht.s),
training_sample=hl.literal(list(train_fit.s)).contains(pops_ht.s),
assign_pops_from_pc_params=hl.struct(min_assignment_prob=min_prob)
)

if not fit:
pops_ht = pops_ht.annotate_globals(
assign_pops_from_pc_params=pops_ht.assign_pops_from_pc_params.annotate(
error_rate=error_rate
)
)

pops_ht = pops_ht.annotate(
evaluation_sample=hl.literal(list(evaluate_fit.s)).contains(pops_ht.s),
training_sample=hl.literal(list(train_fit.s)).contains(pops_ht.s),
)
return pops_ht, pop_clf
else:
return pop_pc_pd, pop_clf
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