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Delete Utilities/for_trees/ColorByClade_v2.0.py
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Auden Cote-L'Heureux
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#Author, date: Auden Cote-L'Heureux, last updated Aug 1st 2023
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#Motivation: Visualize placement of taxa by taxonomic group in trees
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#Intent: Color tip labels in trees by taxonomic group
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#Dependencies: Python3, ete3
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#Inputs: A folder of trees
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#Outputs: a folder of colored trees
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#Example: python ColorByClade_v2.0.py -i /path/to/trees
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import os, sys
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import ete3
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import argparse
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#Needed for communicating with Figtree program
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figtree_format = '''begin figtree;
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set appearance.backgroundColorAttribute="Default";
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set appearance.backgroundColour=#ffffff;
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set appearance.branchColorAttribute="User selection";
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set appearance.branchColorGradient=false;
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set appearance.branchLineWidth=1.0;
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set appearance.branchMinLineWidth=0.0;
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set appearance.branchWidthAttribute="Fixed";
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set appearance.foregroundColour=#000000;
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set appearance.hilightingGradient=false;
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set appearance.selectionColour=#2d3680;
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set branchLabels.colorAttribute="User selection";
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set branchLabels.displayAttribute="Branch times";
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set branchLabels.fontName="sansserif";
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set branchLabels.fontSize=8;
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set branchLabels.fontStyle=0;
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set branchLabels.isShown=false;
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set branchLabels.significantDigits=4;
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set layout.expansion=0;
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set layout.layoutType="RECTILINEAR";
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set layout.zoom=0;
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set legend.attribute=null;
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set legend.fontSize=10.0;
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set legend.isShown=false;
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set legend.significantDigits=4;
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set nodeBars.barWidth=4.0;
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set nodeBars.displayAttribute=null;
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set nodeBars.isShown=false;
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set nodeLabels.colorAttribute="User selection";
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set nodeLabels.displayAttribute="Node ages";
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set nodeLabels.fontName="sansserif";
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set nodeLabels.fontSize=8;
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set nodeLabels.fontStyle=0;
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set nodeLabels.isShown=false;
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set nodeLabels.significantDigits=4;
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set nodeShape.colourAttribute="User selection";
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set nodeShape.isShown=false;
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set nodeShape.minSize=10.0;
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set nodeShape.scaleType=Width;
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set nodeShape.shapeType=Circle;
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set nodeShape.size=4.0;
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set nodeShape.sizeAttribute="Fixed";
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set polarLayout.alignTipLabels=false;
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set polarLayout.angularRange=0;
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set polarLayout.rootAngle=0;
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set polarLayout.rootLength=100;
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set polarLayout.showRoot=true;
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set radialLayout.spread=0.0;
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set rectilinearLayout.alignTipLabels=false;
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set rectilinearLayout.curvature=0;
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set rectilinearLayout.rootLength=100;
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set scale.offsetAge=0.0;
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set scale.rootAge=1.0;
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set scale.scaleFactor=1.0;
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set scale.scaleRoot=false;
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set scaleAxis.automaticScale=true;
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set scaleAxis.fontSize=8.0;
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set scaleAxis.isShown=false;
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set scaleAxis.lineWidth=1.0;
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set scaleAxis.majorTicks=1.0;
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set scaleAxis.origin=0.0;
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set scaleAxis.reverseAxis=false;
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set scaleAxis.showGrid=true;
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set scaleBar.automaticScale=true;
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set scaleBar.fontSize=10.0;
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set scaleBar.isShown=true;
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set scaleBar.lineWidth=1.0;
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set scaleBar.scaleRange=0.0;
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set tipLabels.colorAttribute="User selection";
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set tipLabels.displayAttribute="Names";
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set tipLabels.fontName="sansserif";
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set tipLabels.fontSize=8;
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set tipLabels.fontStyle=0;
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set tipLabels.isShown=true;
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set tipLabels.significantDigits=4;
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set trees.order=false;
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set trees.orderType="increasing";
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set trees.rooting=false;
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set trees.rootingType="User Selection";
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set trees.transform=false;
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set trees.transformType="cladogram";
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end;'''
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def get_args():
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parser = argparse.ArgumentParser(
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prog = 'Tree-coloring script, Version 2.0',
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description = "Updated Aug 1st, 2023 by Auden Cote-L'Heureux"
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)
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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)')
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parser.add_argument('-k', '--keyfile', type = str, help = 'Path to a text file with two tab-separated columns; the first a set of keys and the second a color for each key in hex-code format. Any sequence starting with a particular key will be assigned the color corresponding to that key in this file.')
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return parser.parse_args()
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#Function to extract newick string from either newick or nexus file
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def get_newick(fname):
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newick = ''
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for line in open(fname):
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line = line.split(' ')[-1]
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if(line.startswith('(') or line.startswith('tree1=')):
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newick = line.split('tree1=')[-1].replace("'", '').replace('\\', '')
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return newick
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def reroot(tree):
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#This nested function returns the largest clade of a given taxonomic group
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def get_best_clade(taxon):
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best_size = 0; best_clade = []; seen_leaves = []
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#Traverse all nodes
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for node in tree.traverse('levelorder'):
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#If the node is big enough and not subsumed by a node we've already accepted
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if len(node) >= 3 and len(list(set(seen_leaves) & set([leaf.name for leaf in node]))) == 0:
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leaves = [leaf.name for leaf in node]
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#Create a record of leaves that belong to the taxonomic group
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target_leaves = set()
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for leaf in leaves[::-1]:
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if leaf[:2] in taxon:
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target_leaves.add(leaf[:10])
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leaves.remove(leaf)
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#If this clade is better than any clade we've seen before, grab it
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if len(target_leaves) > best_size and len(leaves) <= 2:
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best_clade = node
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best_size = len(target_leaves)
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seen_leaves.extend([leaf.name for leaf in node])
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return best_clade
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#Get the biggest clade for each taxonomic group (stops once it finds one)
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for taxon in [('Ba', 'Za'), ('Op'), ('Pl'), ('Am'), ('Ex'), ('Sr')]:
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clade = get_best_clade(taxon)
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if len([leaf for leaf in clade if leaf.name[:2] in taxon]) > 3:
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tree.set_outgroup( clade)
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break
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return tree
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def write_lines(o, newick, taxa_and_colors, tree_font_size):
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ntax = str(len(taxa_and_colors))
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#writes the header to the tree file
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o.write('#NEXUS\n')
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o.write('begin taxa;\n')
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o.write('\tdimensions ntax=' + ntax + ';\n')
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o.write('\ttaxlabels\n')
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#write out all taxa
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for taxon in taxa_and_colors:
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o.write('\t' + taxon + '\n')
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o.write(';\nend;\n\n')
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o.write('begin trees;\n')
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o.write('\ttree tree_1 = [&R]\n')
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o.write(newick)
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o.write('end;\n\n')
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for line in figtree_format:
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if('.fontSize' in line):
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o.write(line.replace('8', tree_font_size))
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else:
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o.write(line)
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def write_nexus(newick, leaf_colors, params):
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with open(out_path, 'w') as o:
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write_lines(o, newick, taxa_and_colors, tree_font_size)
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def color(file, args):
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if args.keyfile != None:
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if os.path.isfile(args.keyfile):
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try:
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colors = { line.split('\t')[0] : line.split('\t')[1].strip() for line in open(args.keyfile) if len(line.split('\t')) == 2 }
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except:
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print('\nERROR: your keyfile is incorrectly formatted\n')
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exit()
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else:
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print('\nERROR: your input keyfile could not be found\n')
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else:
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colors = { 'Ba' : '[&!color=#000000]', 'Za' : '[&!color=#808080]', 'Sr' : '[&!color=#7b2516]', 'Op' : '[&!color=#12aaff]', 'Pl' : '[&!color=#006300]', 'Ex' : '[&!color=#ffa100]', 'EE' : '[&!color=#ff6288]', 'Am' : '[&!color=#aa00ff]' }
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newick = get_newick(file)
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tree = ete3.Tree(newick)
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majs = list(dict.fromkeys([leaf.name[:2] for leaf in tree]))
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#Only try to reroot trees with more than 2 major clades. This was added to fix the ETE3 "Cannot set myself as outgroup" error
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if len(majs) > 2:
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tree = reroot(tree)
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tree.ladderize()
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leaf_colors = []
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for leaf in tree:
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keys = sorted([key for key in colors if leaf.name.startswith(key)], key = lambda x : -len(x))
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if len(keys) > 0:
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if '[&!color=' in colors[keys[0]]:
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leaf_colors.append(leaf.name + colors[keys[0]])
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else:
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leaf_colors.append(leaf.name + '[&!color=' + colors[keys[0]] + ']')
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else:
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leaf_colors.append(leaf.name)
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with open('ColoredTrees/' + file.split('/')[-1].split('.tree')[0] + '_Colored.tree', 'w') as o:
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write_lines(o, newick, leaf_colors, str(12))#change tree font size here (right now it is 12)
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if __name__ == '__main__':
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args = get_args()
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if not os.path.isdir('ColoredTrees'):
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os.mkdir('ColoredTrees')
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for tree in os.listdir(args.input):
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if tree.split('.')[-1] in ('tree', 'tre', 'treefile', 'nex'):
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color(args.input + '/' + tree, args)
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