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Update CladeGrabbing_v2.1.py

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Katzlab 2024-02-14 17:46:48 -05:00 committed by GitHub
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Utilities/for_trees/CladeGrabbing_v2.1.py
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@ -25,7 +25,7 @@ def get_args():
parser.add_argument('-t', '--target', type = str, required = True, help = 'A comma-separated list of any number of digits/characters to describe focal taxa (e.g. Sr_ci_S OR Am_t), or a file with the extension .txt containing a list of complete or partial taxon codes. All sequences containing the complete/partial code will be identified as belonging to target taxa.')
parser.add_argument('-m', '--min_presence', type = int, required = True, help = 'Minimum number of target taxa present in clade for it to be selected')
parser.add_argument('-a', '--at_least', type = str, default = '', help = 'A comma-separated list of any number of digits/characters (e.g. Sr_ci_S OR Am_t), or a file with the extension .txt containing a list of complete or partial taxon codes, to describe taxa that MUST be present in a clade for it to be selected (e.g. you may want at least one whole genome).')
parser.add_argument('-na', '--n_at_least', type = int, default = 0, help = 'The number of species belonging to taxa in the --at_least list that must be present in the clade. Default is 1.')
parser.add_argument('-na', '--n_at_least', type = int, default = 0, help = 'The number of species belonging to taxa in the --at_least list that must be present in the clade. Default is 0.')
parser.add_argument('-o', '--outgroup', type = str, default = '', help = 'A comma-separated list of any number of digits/characters (e.g. Sr_ci_S OR Am_t), or a file with the extension .txt containing a list of complete or partial taxon codes, to describe taxa that will be included as outgroups in the output unaligned fasta files (which will contain only sequences from a single selected clade, and all outgroup sequences in the tree captured by this argument).')
parser.add_argument('-c', '--contaminants', type = float, default = 2, help = 'The number of non-ingroup contaminants allowed in a clade, or if less than 1 the proportion of sequences in a clade that can be non-ingroup (i.e. presumed contaminants). Default is to allow 2 contaminants.')