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51 lines
1.4 KiB
Python
51 lines
1.4 KiB
Python
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''' Author, Date : Godwin Ani, 10 - July - 2024.
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Motivation : To make phylogenetic trees more presentable.
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Intent : Shorten the tip labels of phylogenetic trees.
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Dependencies : Python3, ete3
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Inputs : A folder containing trees
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Outputs : A folder of trees with shortened tips.
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python3 RenameTips_v1.0.py -i input to_folder_of_trees
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'''
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import os, re, sys, argparse, string
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import ete3
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parser = argparse.ArgumentParser()
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parser.add_argument('-i', '--input')
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args = parser.parse_args()
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os.makedirs(args.input + '/renamed', exist_ok = True)
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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 tree_formatting_wrapper(file):
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newick = get_newick(file)
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tree = ete3.Tree(newick)
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any_letter = tuple(string.ascii_letters)
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for leaf in tree:
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if leaf.name.startswith(any_letter):
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leaf.name = str(leaf.name).split('_Len')[0]
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leaf.name = str(leaf.name).replace('Contig_', 'Ct')
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leaf.name = str(leaf.name).replace('_XX_0', '')
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tree.write(format=1, outfile=args.input + '/renamed/' +file.split('/')[-1] + '.tree')
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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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tree_formatting_wrapper(args.input + '/' + tree)
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