From 89d67883ad6e066e3e6c89cd6434dde677b1642b Mon Sep 17 00:00:00 2001 From: Lindstnar Date: Thu, 21 Aug 2025 19:59:29 -0700 Subject: [PATCH] fix: preserve taxonomic separators in feature names - Remove r'\.' from special character replacement to preserve dot separators - Fixes inconsistent behavior between | and . input separators - Ensures proper taxonomic hierarchy recognition in all cases --- lefse/lefse_format_input.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lefse/lefse_format_input.py b/lefse/lefse_format_input.py index fc16c55..d6098c7 100755 --- a/lefse/lefse_format_input.py +++ b/lefse/lefse_format_input.py @@ -268,7 +268,7 @@ def modify_feature_names(fn): ret = [re.sub(v,"",f) for f in ret] for v in ["/",r'\(',r'\)',r'-',r'\+',r'=',r'{',r'}',r'\[',r'\]', - r',',r'\.',r';',r':',r'\?',r'\<',r'\>',r'\.',r'\,']: + r',',r';',r':',r'\?',r'\<',r'\>',r'\,']: ret = [re.sub(v,"_",f) for f in ret] for v in ["\|"]: