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Adding TrimAl cutoff as parameter

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Auden Cote-L'Heureux 2025-01-09 12:09:36 -05:00 committed by GitHub
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PTL2/Scripts/utils.py
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@ -43,6 +43,7 @@ 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('--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('--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('--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).')
CL = parser.add_argument_group('Contamination loop parameters') CL = parser.add_argument_group('Contamination loop parameters')
CL.add_argument('--contamination_loop', default = None, choices = {'seq', 'clade', 'both'}, help = 'Remove sequences by looking at the sisters of each sequence in a rules file or by picking the best clades') CL.add_argument('--contamination_loop', default = None, choices = {'seq', 'clade', 'both'}, help = 'Remove sequences by looking at the sisters of each sequence in a rules file or by picking the best clades')