From 4f5bce59634e716f8364575762f8295cfe229cfa Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Sun, 12 Jan 2025 12:35:05 -0500 Subject: [PATCH] Update utils.py --- PTL2/Scripts/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/PTL2/Scripts/utils.py b/PTL2/Scripts/utils.py index c81371c..cf1c115 100644 --- a/PTL2/Scripts/utils.py +++ b/PTL2/Scripts/utils.py @@ -28,7 +28,7 @@ def get_params(): common.add_argument('--data', help = 'Path to the input dataset. The format of this varies depending on your --start parameter. If you are running the contamination loop starting with trees, this folder must include both trees AND a fasta file for each tree (with identical file names other than the extension) that includes an amino-acid sequence for each tip of the tree (with the sequence names matching exactly the tip names).') common.add_argument('--output', default = './', help = 'Directory where the output folder should be created. If not given, the folder will be created in the parent directory of the folder containing the scripts.') common.add_argument('--force', action = 'store_true', help = 'Overwrite all existing files in the "Output" folder.') - common.add_argument('--tree_method', default = 'iqtree', choices = {'iqtree', 'raxml', 'all'}, help = 'Program to use for tree-building') + common.add_argument('--tree_method', default = 'iqtree', choices = {'iqtree', 'iqtree_fast', 'raxml', 'all'}, help = 'Program to use for tree-building') common.add_argument('--blacklist', type = str, help = 'A text file with a list of sequence names not to consider') common.add_argument('--og_identifier', default = 'OG', choices = {'OG','OG6','OGA','OGG'}, help = 'Program to use for selecting seq by GC width') common.add_argument('--sim_taxa', default = None, help = 'Path to the file with the taxa (10-digit codes) to apply the similarity filter on.') @@ -124,7 +124,7 @@ def clean_up(params): if params.end == 'trees' or params.contamination_loop != None: os.mkdir(params.output + '/Output/Trees') os.mkdir(params.output + '/Output/ColoredTrees') - if params.start == 'trees': + if params.start == 'trees' and params.contamination_loop == None: copy_input('Trees')