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Delete Utilities/for_trees/CladeSizes_v2.0.py
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Auden Cote-L'Heureux
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#Author, date: Auden Cote-L'Heureux, last updated Dec 1st 2023
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#Motivation: Understand the topology of trees
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#Intent: Describe clade sizes for different taxonomic groups
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#Dependencies: Python3, ete3
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#Inputs: A folder of trees
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#Outputs: a spreadsheet describing clade sizes
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#Example: python CladeSizes_v2.0.py -i /path/to/trees
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import os, sys, re
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import ete3
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import argparse
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from tqdm import tqdm
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#Extract Newick string
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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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#This function reroots the tree on the largest Ba/Za clade. If there is no prokaryote clade,
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#it roots on the largest Op clade, then Pl, then Am, then Ex, then Sr.
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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 get_clades(file):
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newick = get_newick(file)
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tree = ete3.Tree(newick)
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#Root tree if possible
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try:
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tree = reroot(tree)
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except:
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print('\nUnable to re-root the tree ' + file + ' (maybe it had only 1 major clade, or an inconvenient polytomy). Skipping this step and continuing to try to grab robust clades from the tree.\n')
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majs = list(dict.fromkeys([leaf.name[:2] for leaf in tree]))
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mins = list(dict.fromkeys([leaf.name[:5] for leaf in tree]))
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#For each major and minor clade, find all monophyletic clades of that taxon
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clades_per_tax = { }
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for clade_code in majs + mins:
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clades_per_tax.update({ clade_code : [] })
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seen_leaves = []
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for node in tree.traverse('levelorder'):
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if 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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target_leaves = set()
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for leaf in leaves[::-1]:
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if leaf.startswith(clade_code):
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target_leaves.add(leaf[:10])
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if len(target_leaves) == len(leaves):
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clades_per_tax[clade_code].append(len(list(dict.fromkeys([l[:10] for l in target_leaves]))))
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seen_leaves.extend([leaf.name for leaf in node])
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clades_per_tax = { clade : sorted(clades_per_tax[clade], key = lambda x : -x ) for clade in clades_per_tax }
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return clades_per_tax
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#Write the output spreadsheet
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def write_output(clades_per_tax_per_file):
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clades = sorted(list(dict.fromkeys([clade for file in clades_per_tax_per_file for clade in clades_per_tax_per_file[file] if len(clade) == 2]))) + sorted(list(dict.fromkeys([clade for file in clades_per_tax_per_file for clade in clades_per_tax_per_file[file] if len(clade) == 5])))
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with open('CladeSizesPerTaxon.csv', 'w') as o:
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o.write('OG,' + ','.join(clades) + '\n')
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for tree_file in clades_per_tax_per_file:
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o.write(tree_file)
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for clade in clades:
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if clade in clades_per_tax_per_file[tree_file]:
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if len(clades_per_tax_per_file[tree_file][clade]) > 1:
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o.write(',' + ' '.join(['(' + str(size) + ')' for size in clades_per_tax_per_file[tree_file][clade]]))
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elif len(clades_per_tax_per_file[tree_file][clade]) == 1:
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o.write(',' + str(clades_per_tax_per_file[tree_file][clade][0]))
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else:
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o.write(',')
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else:
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o.write(',')
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o.write('\n')
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(
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prog = 'Clade sizes utility version 2.0',
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description = "Updated Dec 1, 2023 by Auden Cote-L'Heureux"
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)
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parser.add_argument('-i', '--input', required = True, help = 'Path to folder of tree files')
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args = parser.parse_args()
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clades_per_tax_per_file = { }
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for tree_file in tqdm(os.listdir(args.input)):
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if tree_file.split('.')[-1] in ('tre', 'tree', 'treefile', 'nex'):
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clades_per_tax = get_clades(args.input + '/' + tree_file)
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clades_per_tax_per_file.update({ tree_file.split('.')[0] : clades_per_tax })
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write_output(clades_per_tax_per_file)
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