From 7b3860a4492d2e5ba0ac7b036bc84cdbe6610a50 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Fri, 13 Oct 2023 10:09:16 -0400 Subject: [PATCH] Update utils.py --- 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 c0af141..0177262 100644 --- a/PTL2/Scripts/utils.py +++ b/PTL2/Scripts/utils.py @@ -24,7 +24,7 @@ def get_params(): core = parser.add_argument_group('Core parameters (rarely altered from the defaults)') core.add_argument('--blast_cutoff', default = 1e-20, type = float, help = 'Blast e-value cutoff') core.add_argument('--len_cutoff', default = 10, type = int, help = 'Amino acid length cutoff for removal of very short sequences after column removal in Guidance.') - core.add_argument('--sim_cutoff', default = 0.98, type = float, help = 'Sequences from the same taxa that are assigned to the same OG are removed if they are more similar than this cutoff') + core.add_argument('--sim_cutoff', default = 1, type = float, help = 'Sequences from the same taxa that are assigned to the same OG are removed if they are more similar than this cutoff') core.add_argument('--overlap_cutoff', default = 0.35, type = float, help = 'A sequence is removed if its alignment length to the longest sequence in its OG & taxon is less than this proportion of the length of the longest sequence') core.add_argument('--guidance_iters', default = 5, type = int, help = 'Number of Guidance iterations for sequence removal') core.add_argument('--seq_cutoff', default = 0.3, type = float, help = 'During guidance, taxa are removed if their score is below this cutoff')