From 426d51ea858c89bfdc7f69157662f41b1ecae956 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Wed, 29 May 2024 12:44:15 -0400 Subject: [PATCH] Changing default output location in 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 32e5158..1fe26c8 100644 --- a/PTL2/Scripts/utils.py +++ b/PTL2/Scripts/utils.py @@ -26,7 +26,7 @@ def get_params(): common.add_argument('--gf_list', default = None, help = 'Path to the file with the GFs of interest. Only required if starting from the raw dataset.') common.add_argument('--taxon_list', default = None, help = 'Path to the file with the taxa (10-digit codes) to include in the output.') 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('--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('--blacklist', type = str, help = 'A text file with a list of sequence names not to consider')