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Update CladeGrabbing_v2.1.py

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Katzlab 2024-01-29 08:20:30 -05:00 committed by GitHub
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1 changed files with 3 additions and 2 deletions
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Utilities/for_trees/CladeGrabbing_v2.1.py
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@ -5,6 +5,7 @@
#Inputs: A folder of trees and corresponding unaligned .fasta files #Inputs: A folder of trees and corresponding unaligned .fasta 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_v2.1.py --input /Path/to/trees --target Sr_rh --min_presence 20 #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 #Dependencies
import os, re, sys import os, re, sys
@ -19,7 +20,7 @@ def get_args():
prog = 'Clade grabber, Version 2.1', prog = 'Clade grabber, Version 2.1',
description = "Updated Aug 1st, 2023 by Auden Cote-L'Heureux" 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('-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('-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('-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() main()