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Utils script with sim taxa and OG identifier flag

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Godwin Ani 2023-12-04 15:00:10 -05:00 committed by GitHub
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commit 304cebc73f
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1 changed files with 3 additions and 1 deletions
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PTL2/Scripts/utils.py
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@ -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('--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', '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('--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 = 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('--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.') 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.')