YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-27 07:50:25 +08:00
Code Issues Packages Projects Releases Wiki Activity

Update CladeSizes.py

Browse Source 
Modified to work with clade grabbed input file names.
This commit is contained in:
Adri K. Grow 2024-11-11 08:59:47 -05:00 committed by GitHub
parent fb6e7aa6e7
commit a0b45ed2c8
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
1 changed files with 5 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
Utilities/for_trees/CladeSizes.py
View File

@ -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)