From 33d73c1dc5913c6b828389a1ccd4e4fddcd7077d Mon Sep 17 00:00:00 2001 From: Bogdan Kirilenko Date: Thu, 13 Apr 2023 22:37:17 +0200 Subject: [PATCH] Fixing accidental dinucleotides in the codon.fasta output --- CESAR_wrapper.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CESAR_wrapper.py b/CESAR_wrapper.py index 29cc81e..9bb5b37 100755 --- a/CESAR_wrapper.py +++ b/CESAR_wrapper.py @@ -1845,6 +1845,10 @@ def extract_codon_data(codon_table, excl_exons=None): que_subcodons = [GAP_CODON for x in range(len(ref_subcodons))] t_codons.extend(ref_subcodons) q_codons.extend(que_subcodons) + elif ref_codon == "-" or ref_codon == "--": + # special case to be captured Apr 2023 + t_codons.append(GAP_CODON) + q_codons.append(XXX_CODON) else: # something strange ref_int = check_codon(ref_codon[-3:])