From baf5fd037dae1fdc84c009dd900318d4d89bcc5c Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Thu, 9 Jan 2025 12:09:36 -0500 Subject: [PATCH] Adding TrimAl cutoff as parameter --- PTL2/Scripts/utils.py | 1 + 1 file changed, 1 insertion(+) diff --git a/PTL2/Scripts/utils.py b/PTL2/Scripts/utils.py index 23200ca..11ad13f 100644 --- a/PTL2/Scripts/utils.py +++ b/PTL2/Scripts/utils.py @@ -43,6 +43,7 @@ def get_params(): core.add_argument('--col_cutoff', default = 0.0, type = float, help = 'During guidance, columns are removed if their score is below this cutoff') core.add_argument('--res_cutoff', default = 0.0, type = float, help = 'During guidance, residues are removed if their score is below this cutoff') core.add_argument('--guidance_threads', default = 20, type = int, help = 'Number of threads to allocate to Guidance') + core.add_argument('--trimal_cutoff', default = 0.05, type = float, help = 'Gap masking threshold for TrimAl. The maximum proportion of sequences without gaps for a site to be removed (i.e. to remove sites with 95% or more gaps, set this parameter to 0.05).') 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')