For adding metadata to tree tip labels

Utilities/for_trees/rename_tip_labels .py

@@ -0,0 +1,39 @@
+
+''' Author, Date : Godwin Ani, 15th - September - 2023.
+Motivation : To make phylogenetic trees more presentable.
+Intent : Rename the tip labels of phylogenetic trees.
+Dependencies : Python3, Pandas
+Inputs : A folder containing trees and a csv file(with headers).
+The first column of the csv is the 10 digit code and other columns are the information to be added to the tip labels.
+Outputs : A folder of trees with renamed tips.
+python3 rename_tip_labels.py -i input to_folder_of_trees -s to_spreadsheet
+'''
+
+import os, re, sys, argparse
+import pandas as pd
+parser = argparse.ArgumentParser()
+parser.add_argument('-i', '--input')
+parser.add_argument('-s', '--spreadsheet')
+args = parser.parse_args()
+os.makedirs(args.input + '/renamed', exist_ok = True)
+df = pd.read_csv(args.spreadsheet)
+df = df.astype(str)
+df['Merged'] = df.apply(lambda row: '_'.join(row), axis=1)
+for file in os.listdir(args.input):
+    if file.endswith('.tree') or file.endswith('.tre'):
+        with open(args.input + '/' + file, 'r') as tree:
+            tree = tree.read()
+            tree = tree.replace('Len_', 'L')
+            tree = tree.replace('Cov_', 'Cv')
+            tree = tree.replace('Contig_', 'Ct')
+            tree = tree.replace('Len', 'L')
+            tree = tree.replace('Cov', 'Cv')
+            tree = tree.replace('Contig', 'Ct')
+            search_strings = df.iloc[:, 0].tolist()
+            replacement_strings = df['Merged'].tolist()
+            for search, replace in zip(search_strings, replacement_strings):
+                tree = tree.replace(search,replace)
+                with open(args.input + '/renamed/' + file, 'w') as o:
+                    o.write(tree)
+
+