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Update utils.py

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Godwin N. Ani 2025-07-17 14:46:52 -04:00 committed by GitHub
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PTL2/Scripts/utils.py
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@ -44,7 +44,7 @@ def get_params():
core.add_argument('--col_cutoff', default = 0.0, type = float, help = 'During guidance, columns are removed if their score is below this cutoff')
core.add_argument('--res_cutoff', default = 0.0, type = float, help = 'During guidance, residues are removed if their score is below this cutoff')
core.add_argument('--guidance_threads', default = 20, type = int, help = 'Number of threads to allocate to Guidance')
core.add_argument('--trimal_cutoff', default = 0.05, type = float, help = 'Gap masking threshold for TrimAl. The maximum proportion of sequences without gaps for a site to be removed (i.e. to remove sites with 95% or more gaps, set this parameter to 0.05).')
core.add_argument('--trimal_cutoff', default = 0.3, type = float, help = 'Gap masking threshold for TrimAl. The maximum proportion of sequences without gaps for a site to be removed (i.e. to remove sites with 70% or more gaps, set this parameter to 0.3).')
core.add_argument('--allow_large_files', action = 'store_true', help = 'Allow files with more than 2,000 sequences to run through Guidance.')
CL = parser.add_argument_group('Contamination loop parameters')