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Update CladeSizes.py

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Modified to work with clade grabbed input file names.
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Adri K. Grow 2024-11-11 08:59:47 -05:00 committed by GitHub
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1 changed files with 5 additions and 4 deletions
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Utilities/for_trees/CladeSizes.py
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@ -1,4 +1,4 @@
#Author, date: Auden Cote-L'Heureux, last updated Dec 18th 2023 #Author, date: Auden Cote-L'Heureux, last updated Nov 11th 2024 by Adri Grow
#Motivation: Understand the topology of trees #Motivation: Understand the topology of trees
#Intent: Describe clade sizes for different taxonomic groups #Intent: Describe clade sizes for different taxonomic groups
#Dependencies: Python3, ete3 #Dependencies: Python3, ete3
@ -236,9 +236,10 @@ if __name__ == '__main__':
for tree_file in tqdm(os.listdir(args.input)): for tree_file in tqdm(os.listdir(args.input)):
if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex'): if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex'):
clades_per_tax, majs_per_clade, mins_per_clade = get_clades(args.input + '/' + tree_file, args) clades_per_tax, majs_per_clade, mins_per_clade = get_clades(args.input + '/' + tree_file, args)
clades_per_tax_per_file.update({ tree_file.split('.')[0] : clades_per_tax }) base_filename = os.path.splittext(tree_file)[0]
majs_per_clade_per_file.update({ tree_file.split('.')[0] : majs_per_clade }) clades_per_tax_per_file.update({ base_filename : clades_per_tax })
mins_per_clade_per_file.update({ tree_file.split('.')[0] : mins_per_clade }) majs_per_clade_per_file.update({ base_filename : majs_per_clade })
mins_per_clade_per_file.update({ base_filename : mins_per_clade })
write_output(clades_per_tax_per_file, args, majs_per_clade = majs_per_clade_per_file, mins_per_clade = mins_per_clade_per_file) write_output(clades_per_tax_per_file, args, majs_per_clade = majs_per_clade_per_file, mins_per_clade = mins_per_clade_per_file)