diff --git a/Utilities/for_trees/CladeGrabbing_v2.1.py b/Utilities/for_trees/CladeGrabbing_v2.1.py index d70fade..497f611 100644 --- a/Utilities/for_trees/CladeGrabbing_v2.1.py +++ b/Utilities/for_trees/CladeGrabbing_v2.1.py @@ -5,6 +5,7 @@ #Inputs: A folder of trees and corresponding unaligned .fasta files #Outputs: A folder of grabbed clades and filtered unaligned fasta files #Example: python CladeGrabbing_v2.1.py --input /Path/to/trees --target Sr_rh --min_presence 20 +#IMPORTANT: key parameters explained in "add_argument" section below #Dependencies import os, re, sys @@ -19,7 +20,7 @@ def get_args(): prog = 'Clade grabber, Version 2.1', description = "Updated Aug 1st, 2023 by Auden Cote-L'Heureux" ) - +#add_argument section with parameters explained parser.add_argument('-i', '--input', type = str, required = True, help = 'Path to a folder containing input trees (which must have the file extension .tre, .tree, .treefile, or .nex)') 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') @@ -218,4 +219,4 @@ def main(): main() - \ No newline at end of file +