From d3c870d4ad41679d5fba486c7bbd4808352efe1c Mon Sep 17 00:00:00 2001 From: ViralVerity Date: Tue, 5 Sep 2023 14:28:57 -0400 Subject: [PATCH] change serotype call to be always on untrimmed coverage --- denv_pipeline/scripts/serotype_caller.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/denv_pipeline/scripts/serotype_caller.py b/denv_pipeline/scripts/serotype_caller.py index 8bf6507..f10e940 100755 --- a/denv_pipeline/scripts/serotype_caller.py +++ b/denv_pipeline/scripts/serotype_caller.py @@ -67,7 +67,6 @@ def populate_line(args): seq_trim = sequence[trim_pos[0]-1:trim_pos[1]] perc_cov_trim = calculate_coverage(seq_trim, amb_list)[0] - perc_cov_relevant = perc_cov_trim with open(args.alignment.replace(".out.aln",".out.trim.aln"), 'w') as new_file: SeqIO.write(seq_trim, new_file, 'fasta') @@ -77,9 +76,8 @@ def populate_line(args): else: perc_cov_trim = "NA" - perc_cov_relevant = perc_cov - if perc_cov_relevant>=min_coverage: + if perc_cov>=min_coverage: write_dict["serotype_called"] = serotype else: write_dict["serotype_called"] = "NA"