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Update CladeGrabbing_v3.2.py

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Adri K. Grow 2024-06-03 14:50:00 -04:00 committed by GitHub
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Utilities/for_trees/CladeGrabbing_v3.2.py
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#Motivation: Select robust sequences from trees #Motivation: Select robust sequences from trees
#Intent: Select clades of interest from large trees using taxonomic specifications #Intent: Select clades of interest from large trees using taxonomic specifications
#Dependencies: Python3, ete3, Biopython #Dependencies: Python3, ete3, Biopython
#Inputs: A folder of trees and corresponding unaligned .fasta files #Inputs: A folder containing: all PTLp2 output trees and all corresponding unaligned .fasta (pre-guidance) files
#Outputs: A folder of grabbed clades and filtered unaligned fasta files #Outputs: A folder of grabbed clades and filtered unaligned fasta files
#Example: python CladeGrabbing_v3.2.py --input /Path/to/trees --target Sr_rh --min_presence 20 #Example: python CladeGrabbing_v3.2.py --input /Path/to/trees --target Sr_rh --min_presence 20
#IMPORTANT: key parameters explained in "add_argument" section below #IMPORTANT: key parameters explained in "add_argument" section below