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