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Update utils.py

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Auden Cote-L'Heureux 2025-01-12 12:35:05 -05:00 committed by GitHub
parent d595a51b4f
commit 4f5bce5963
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1 changed files with 2 additions and 2 deletions
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PTL2/Scripts/utils.py
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@ -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')