From 8f03c6c9d4113430966d949ccadc46c82a8f2ca1 Mon Sep 17 00:00:00 2001 From: joshuailevy Date: Mon, 29 Jan 2024 12:00:59 -0800 Subject: [PATCH] mutation frequency keyword added, closes #36 --- src/outbreak_data/outbreak_data.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/outbreak_data/outbreak_data.py b/src/outbreak_data/outbreak_data.py index fa238be..c30c7af 100644 --- a/src/outbreak_data/outbreak_data.py +++ b/src/outbreak_data/outbreak_data.py @@ -199,6 +199,8 @@ def lineage_mutations(pango_lin=None, lineage_crumbs=False, mutations=None, freq if mutations: query = '&' + f'mutations={mutations}' + query + if freq!=0.8: + query = query + f'&frequency={freq}' raw_data = get_outbreak_data('genomics/lineage-mutations', f'{query}', collect_all=False) key_list = raw_data['results'] if len(key_list) == 0: @@ -208,11 +210,7 @@ def lineage_mutations(pango_lin=None, lineage_crumbs=False, mutations=None, freq key_list = list(key_list) df = pd.DataFrame(raw_data['results'][key_list[0]]) - if freq != 0.8: - if isinstance(freq, float) and freq > 0 and freq < 1: - return df.loc[df['prevalence'] >= freq] - else: - return df + return df def global_prevalence(pango_lin, mutations=None, cumulative=None, lineage_crumbs=False, server=server):