From d161957d86d441bc12b12fae76c09376a922aef4 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Fri, 28 Mar 2025 15:40:58 -0400 Subject: [PATCH] Taking out 'both' option of contamination loop --- PTL2/Scripts/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PTL2/Scripts/utils.py b/PTL2/Scripts/utils.py index f2ef4d4..9a5710b 100644 --- a/PTL2/Scripts/utils.py +++ b/PTL2/Scripts/utils.py @@ -47,7 +47,7 @@ def get_params(): core.add_argument('--allow_large_files', action = 'store_true', help = 'Allow files with more than 2,000 sequences to run through Guidance.') CL = parser.add_argument_group('Contamination loop parameters') - CL.add_argument('--contamination_loop', default = None, choices = {'seq', 'clade', 'both'}, help = 'Remove sequences by looking at the sisters of each sequence in a rules file or by picking the best clades') + CL.add_argument('--contamination_loop', default = None, choices = {'seq', 'clade'}, help = 'Remove sequences by looking at the sisters of each sequence in a rules file or by picking the best clades') CL.add_argument('--nloops', default = 10, type = int, help = 'The maximum number of contamination-removal loops') CL.add_argument('--cl_tree_method', default = 'fasttree', choices = {'iqtree', 'raxml', 'fasttree', 'iqtree_fast'}, help = 'Tree-building method to use in each contamination loop iteration.') CL.add_argument('--cl_alignment_method', default = 'mafft_only', choices = {'mafft_only', 'guidance'}, help = 'Alignment method to use in each contamination loop iteration.')