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Update ColorByClade.py

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added example use and note on how to turn off rooting
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Katzlab 2024-07-16 09:23:57 -04:00 committed by GitHub
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commit 20e38f57b5
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1 changed files with 5 additions and 2 deletions
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Utilities/for_trees/ColorByClade.py
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@ -1,10 +1,12 @@
#Author, date: Auden Cote-L'Heureux & Godwin Ani, last updated Feb 21st 2024 #Author, date: Auden Cote-L'Heureux & Godwin Ani & LAK, last updated July 16 2024
#Motivation: Visualize placement of taxa by taxonomic group in trees #Motivation: Visualize placement of taxa by taxonomic group in trees
#Intent: Color tip labels in trees by taxonomic group #Intent: Color tip labels in trees by taxonomic group
#Dependencies: Python3, ete3 #Dependencies: Python3, ete3
#Inputs: A folder of trees #Inputs: A folder of trees
#Outputs: a folder of colored trees #Outputs: a folder of colored trees
#Example: python ColorByClade_v2.1.py -i /path/to/trees #Example: python ColorByClade_v2.1.py -i /path/to/trees
#Example: python ColorByClade_v2.1.py -i /path/to/trees -k keys.txt
#NOTE: turn off rooting at lines 227-229 if you want colored unrooted trees
import os, sys, shutil import os, sys, shutil
@ -220,7 +222,8 @@ def tree_formatting_wrapper(file):
majs = list(dict.fromkeys([leaf.name[:2] for leaf in tree])) majs = list(dict.fromkeys([leaf.name[:2] for leaf in tree]))
#Only try to reroot trees with more than 2 major clades. This was added to fix the ETE3 "Cannot set myself as outgroup" error #Only try to reroot trees with more than 2 major clades. This was added to fix the ETE3 "Cannot set myself as outgroup" error
#turn off the next three lines to color without rooting
if len(majs) > 2: if len(majs) > 2:
tree = reroot(tree) tree = reroot(tree)
tree.ladderize(direction = 1) tree.ladderize(direction = 1)