fix issue with spaces in mutation strings

andersen-lab · Jun 7, 2023 · 518a323 · 518a323
1 parent 16c0cd7
commit 518a323
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/freyja/read_analysis_tools.py b/freyja/read_analysis_tools.py
@@ -677,6 +677,7 @@ def plot_covariants(covar_file, output, num_clusters, min_mutations, nt_muts):
 
     covars = pd.read_csv(covar_file, sep='\t', header=0)
     covars['Covariants'] = covars['Covariants']\
+        .str.replace(', ', ',')\
         .str.split(' ')\
         .apply(filter_covariants_output, args=(min_mutations, nt_muts))\