From fa1f50e6f09f94d4654e2af9e9b0062649d6d601 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Fri, 18 Apr 2025 08:45:40 -0400 Subject: [PATCH] Update guidance_path param --- 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 e1cd3e9..8f90971 100644 --- a/PTL2/Scripts/utils.py +++ b/PTL2/Scripts/utils.py @@ -39,7 +39,7 @@ def get_params(): core.add_argument('--similarity_filter', action = 'store_true', help = 'Run the similarity filter in pre-Guidance') 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('--guidance_iters', default = 5, type = int, help = 'Number of Guidance iterations for sequence removal') - core.add_argument('--guidance_path', help = 'Path to the downloaded Guidance folder (probably called guidance_Linux or guidance_MacOS-arm64, this folder should contain a folder called "scripts" which contains the guidance_main.py script). You can download this folder from this link: https://github.com/XseniaP/Guidance_mid/tree/main') + core.add_argument('--guidance_path', help = 'Path to the downloaded Guidance folder (probably called guidance_Linux or guidance_MacOS-arm64, this folder should contain a folder called "script" which contains the guidance_main.py script). You can download this folder from this link: https://github.com/XseniaP/Guidance_mid/tree/main') core.add_argument('--seq_cutoff', default = 0.3, type = float, help = 'During guidance, taxa are removed if their score is below this cutoff') 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')