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1 parent b89e20b commit 00656edCopy full SHA for 00656ed
1 file changed
malariagen_data/anoph/frq_base.py
@@ -30,6 +30,8 @@ def _prep_samples_for_cohort_grouping(
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if filter_unassigned is None:
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filter_unassigned = taxon_by == "taxon"
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+ # Filter out samples with "intermediate" or "unassigned" taxon values
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+ # by setting them to None, so they are excluded from cohort grouping.
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if filter_unassigned:
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loc_intermediate_taxon = (
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df_samples[taxon_by].str.startswith("intermediate").fillna(False)
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