From 2b6112335bbd122fa2d498d237a7b0b124e87111 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Fri, 12 Apr 2024 13:39:45 +0100 Subject: [PATCH] reverting the find am script change --- snipit/scripts/snp_functions.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/snipit/scripts/snp_functions.py b/snipit/scripts/snp_functions.py index bb9e6cc..673ff3f 100644 --- a/snipit/scripts/snp_functions.py +++ b/snipit/scripts/snp_functions.py @@ -261,13 +261,10 @@ def find_snps(reference_seq,input_seqs,show_indels): return snp_dict,record_snps,len(var_counter) -def find_ambiguities(alignment,snp_dict,sequence_type): +def find_ambiguities(alignment,snp_dict): + - if sequence_type == "nt": - amb = NT_AMBIG - if sequence_type == "aa": - amb = AA_AMBIG snp_sites = collections.defaultdict(list)