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Godwin Ani 2024-06-04 12:47:49 -04:00 committed by GitHub
parent 405217e2a2
commit fd7b2e7302
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1 changed files with 48 additions and 18 deletions
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66
Utilities/for_trees/ColorByClade.py
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@ -4,10 +4,10 @@
#Dependencies: Python3, ete3
#Inputs: A folder of trees
#Outputs: a folder of colored trees
#Example: python ColorByClade.py -i /path/to/trees
#Example: python ColorByClade_v2.1.py -i /path/to/trees
import os, sys
import os, sys, shutil
import ete3
import argparse
@ -43,7 +43,7 @@ figtree_format = '''begin figtree;
set nodeLabels.colorAttribute="User selection";
set nodeLabels.displayAttribute="Node ages";
set nodeLabels.fontName="sansserif";
set nodeLabels.fontSize=16;
set nodeLabels.fontSize=8;
set nodeLabels.fontStyle=0;
set nodeLabels.isShown=false;
set nodeLabels.significantDigits=4;
@ -83,7 +83,7 @@ figtree_format = '''begin figtree;
set tipLabels.colorAttribute="User selection";
set tipLabels.displayAttribute="Names";
set tipLabels.fontName="sansserif";
set tipLabels.fontSize=16;
set tipLabels.fontSize=12;
set tipLabels.fontStyle=0;
set tipLabels.isShown=true;
set tipLabels.significantDigits=4;
@ -213,6 +213,22 @@ def write_nexus(newick, leaf_colors, params):
write_lines(o, newick, taxa_and_colors, tree_font_size)
def tree_formatting_wrapper(file):
try:
newick = get_newick(file)
tree = ete3.Tree(newick)
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
if len(majs) > 2:
tree = reroot(tree)
tree.ladderize(direction = 1)
tree.write(outfile = 'ColoredTrees/Temp/' + file.split('/')[-1].split('.tree')[0] + '_Colored.tree')
except Exception as e:
print(f" {file.split('/')[-1]} has {e} error ")
def color(file, args):
@ -226,19 +242,11 @@ def color(file, args):
else:
print('\nERROR: your input keyfile could not be found\n')
else:
colors = { 'Ba' : '[&!color=#000000]', 'Za' : '[&!color=#808080]', 'Sr' : '[&!color=#B4A26D]', 'Op' : '[&!color=#c07ba0]', 'Pl' : '[&!color=#026736]', 'Ex' : '[&!color=#E63B60]', 'EE' : '[&!color=#0343FC]', 'Am' : '[&!color=#29C5F6]', 'EE_cr' : '[&!color=#08B461]', 'EE_ha' : '[&!color=#03EA74]', 'Sr_ci' : '[&!color=#A97533]', 'Sr_ap' : '[&!color=#D4BA99]', 'Sr_rh' : '[&!color=#8A3324]', 'Sr_st' : '[&!color=#E97451]', 'Sr_di' : '[&!color=#492815]' }
#tree_formatting_wrapper
try:
newick = get_newick(file)
tree = ete3.Tree(newick)
colors = { 'Ba' : '[&!color=#000000]', 'Za' : '[&!color=#808080]', 'Sr' : '[&!color=#B4A26D]', 'Op' : '[&!color=#1260CC]', 'Pl' : '[&!color=#026736]', 'Ex' : '[&!color=#E63B60]', 'EE' : '[&!color=#C76A6A]', 'Am' : '[&!color=#29C5F6]', 'EE_cr' : '[&!color=#08B461]', 'EE_ha' : '[&!color=#03EA74]', 'Sr_ci' : '[&!color=#A97533]', 'Sr_ap' : '[&!color=#D4BA99]', 'Sr_rh' : '[&!color=#8A3324]', 'Sr_st' : '[&!color=#E97451]', 'Sr_di' : '[&!color=#492815]' }
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
if len(majs) > 2:
tree = reroot(tree)
tree.ladderize(direction = 1)
except Exception as e:
print(f" {file.split('/')[-1]} has {e} error ")
newick = get_newick(file)
tree = ete3.Tree(newick)
leaf_colors = []
for leaf in tree:
@ -255,7 +263,7 @@ def color(file, args):
else:
leaf_colors.append(leaf.name)
with open('ColoredTrees/' + file.split('/')[-1].split('.tree')[0] + '_Colored.tree', 'w') as o:
with open('ColoredTrees/' + file.split('/')[-1].split('.tree')[0] + '.tree', 'w') as o:
write_lines(o, newick, leaf_colors, str(12))#change tree font size here (right now it is 12)
if __name__ == '__main__':
@ -265,7 +273,29 @@ if __name__ == '__main__':
if not os.path.isdir('ColoredTrees'):
os.mkdir('ColoredTrees')
if not os.path.isdir('ColoredTrees/Temp'):
os.mkdir('ColoredTrees/Temp')
for tree in os.listdir(args.input):
if tree.split('.')[-1] in ('tree', 'tre', 'treefile', 'nex'):
color(args.input + '/' + tree, args)
tree_formatting_wrapper(args.input + '/' + tree)
for tree in os.listdir('ColoredTrees/Temp'):
if tree.split('.')[-1] in ('tree', 'tre', 'treefile', 'nex'):
color('ColoredTrees/Temp/' + tree, args)
shutil.rmtree('ColoredTrees/Temp')