diff --git a/sc2ts/utils.py b/sc2ts/utils.py index 0752ce9..6ca999a 100644 --- a/sc2ts/utils.py +++ b/sc2ts/utils.py @@ -393,6 +393,7 @@ def __init__(self, ts, show_progress=True, pango_source="Viridian_pangolin"): # # Corresponding sample-set names for this array # self.pango_lineage_keys = np.array(list(self.pango_lineage_samples.keys())) + def _compute_mutation_stats(self): ts = self.ts @@ -715,7 +716,7 @@ def recombinants_summary(self): for u in df.node: md = self.nodes_metadata[sample_map[u]] causal_strain.append(md["strain"]) - causal_pango.append(md["Nextclade_pango"]) + causal_pango.append(md[self.pango_source]) causal_date.append(md["date"]) df["causal_strain"] = causal_strain df["causal_pango"] = causal_pango @@ -2013,7 +2014,7 @@ def add_gisaid_lineages_to_ts(ts, node_gisaid_lineages, linmuts_dict): return edited_ts -# NOTE: this is broken since moving to Viridian metadata, we no longer have +# NOTE: this is broken since moving to Viridian metadata, we no longer have # GISAID EPI ISL in the metadata def check_lineages( ts,