Shorten tree tip names

Utilities/for_trees/ShortenTips.py

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+
+''' Author, Date : Godwin Ani, 15th - September - 2023.
+Motivation : To make phylogenetic trees more presentable.
+Intent : Shorten the tip labels of phylogenetic trees.
+Dependencies : Python3, ete3
+Inputs : A folder containing trees
+Outputs : A folder of trees with shortened tips.
+python3 RenameTips_v1.0.py -i input to_folder_of_trees 
+'''
+
+
+import os, re, sys, argparse, string
+import ete3
+
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-i', '--input')
+args = parser.parse_args()
+os.makedirs(args.input + '/renamed', exist_ok = True)
+
+def get_newick(fname):
+    newick = ''
+    for line in open(fname):
+        line = line.split(' ')[-1]
+        if(line.startswith('(') or line.startswith('tree1=')):
+            newick = line.split('tree1=')[-1].replace("'", '').replace('\\', '')
+    return newick
+
+
+def tree_formatting_wrapper(file):
+    newick = get_newick(file)
+    tree = ete3.Tree(newick)    
+    any_letter = tuple(string.ascii_letters)
+    for leaf in tree:
+        if leaf.name.startswith(any_letter):
+            leaf.name = str(leaf.name).split('_Len')[0]
+            leaf.name = str(leaf.name).replace('Contig_', 'Ct')
+            leaf.name = str(leaf.name).replace('_XX_0', '')
+    tree.write(format=1, outfile=args.input + '/renamed/' +file.split('/')[-1] + '.tree')
+
+
+for tree in os.listdir(args.input):
+    if tree.split('.')[-1] in ('tree', 'tre', 'treefile', 'nex'):
+        tree_formatting_wrapper(args.input + '/' + tree)
+
+
+
+
+