From 304cebc73f12bfacfa5c84842ccf39949fb397e5 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Mon, 4 Dec 2023 15:00:10 -0500 Subject: [PATCH] Utils script with sim taxa and OG identifier flag --- PTL2/Scripts/utils.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/PTL2/Scripts/utils.py b/PTL2/Scripts/utils.py index 8b9845e..229f363 100644 --- a/PTL2/Scripts/utils.py +++ b/PTL2/Scripts/utils.py @@ -20,7 +20,9 @@ def get_params(): 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') - + common.add_argument('--og_identifier', default = '_OG', choices = {'_OG6','_OGA','_OGG', '_OG'}, 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.') + 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.')