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Update Cluster_v2.0.py
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Godwin Ani
GitHub
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#Professor L. Katz and Godwin Ani
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'''
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#9th- Feb- 2023
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#Author, date: Godwin Ani and Laura Katz, 9th- Feb - 2023.
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#A clustering program that accepts and validates users input
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#Dependencies: Python3, CD-Hit
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#Inputs: A folder of containing Amino acid or DNA fasta files.
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#Outputs: A folder of clustered files.
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#Example: python Cluster_v2.0.py --type dna --identity 0.95 --overlap 0.67 --input input_folder_dna --output output_folder_dna
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'''
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import os, sys, re
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import os
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import argparse
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from tqdm import tqdm
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from tqdm import tqdm
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import subprocess
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def input_validation(value, error_message):
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def cluster():
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''' This function takes an amino acid or DNA sequence stored in a fasta format and clusters it.
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It uses two nested functions (cluster_AA and cluster_DNA) to perform this operation.
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Ensure that fasta files to be clustered are stored in a root directory folder named "to_cluster". This folder will automatically be created if none exists.
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The result of the clustering process is saved into a root directory folder named "Clustered" which is created automatically if none exists. '''
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if not os.path.isdir('to_cluster'):
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os.mkdir('to_cluster')
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if not os.path.isdir('Clustered'):
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os.mkdir('Clustered')
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# Nested function for amino acids clustering.
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def cluster_AA():
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#input validation for the sequence identity threshold.
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while True:
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try:
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try:
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val1 =input( 'Amino Acids Sequence Identity Threshold (e.g. 0.99, 0.95)? : ')
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integer, fractional = value.split('.')
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integer, fractional = val1.split('.')
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value = float(value)
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val1 = float(val1)
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if int(integer) == 0 and len(fractional) == 2:
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if int(integer) == 0 and len(fractional) == 2:
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break
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return value
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except ValueError:
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except ValueError:
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pass
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pass
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print('ERROR! Use format 0.## for Amino acids sequence identity threshold.')
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print(error_message)
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exit(1)
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#Input validation for the overlap value.
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def cluster_sequences(program, threshold, overlap, input_folder, output_folder):
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while True:
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for file in tqdm(os.listdir(input_folder)):
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try:
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val2 =input( 'Amino Acids Alignment Overlap Value (e.g. 0.67, 0.75)? : ')
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integer, fractional = val2.split('.')
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val2 = float(val2)
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if int(integer)== 0 and len(fractional) == 2:
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break
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except ValueError:
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pass
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print('ERROR! Use format 0.## for Amino acids sequence alignment overlap value')
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#Selects amino acids fasta files in "to_cluster" folder and clusters them with CD-HIT.
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for file in tqdm(os.listdir('to_cluster')):
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if file.endswith('.fasta'):
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if file.endswith('.fasta'):
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os.system('cd-hit -i to_cluster/' + file + ' -o Clustered/' + file + ' -c %s -d 0 -aS %s' %( val1, val2))
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subprocess.run([f'{program}', '-i', f'{input_folder}/{file}', '-o', f'{output_folder}/{file}', '-c', f'{threshold}', '-d', '0', '-aS', f'{overlap}'])
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#Renaming the result of the clustering.
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for file in os.listdir('Clustered'):
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for file in os.listdir(output_folder):
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if file.endswith('.clstr'):
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if file.endswith('.clstr'):
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os.rename('Clustered/' + file, 'Clustered/' + file.split('FILE')[0] + 'Clustered.txt')
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os.rename(f'{output_folder}/{file}', f'{output_folder}/{file.split("FILE")[0]}Clustered.txt')
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def main():
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parser = argparse.ArgumentParser(description='Cluster amino acid or DNA sequences using CD-HIT.')
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parser.add_argument('--type', choices=['aa', 'dna'], required=True, help='Type of sequences (aa for Amino Acids, dna for DNA)')
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parser.add_argument('--identity', type=str, required=True, help='Sequence Identity Threshold (e.g., 0.99, 0.95)')
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parser.add_argument('--overlap', type=str, required=True, help='Sequence Alignment Overlap Value (e.g., 0.67, 0.75)')
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parser.add_argument('--input', type=str, required=True, help='Input folder containing sequences in fasta format')
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parser.add_argument('--output', type=str, required=True, help='Output folder for clustered sequences')
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#Nested function for DNA clustering.
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args = parser.parse_args()
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def cluster_DNA():
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#Input validation for the sequence identity threshold.
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while True:
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try:
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val1 =input( 'DNA Sequence Identity Threshold (e.g. 0.99, 0.95)? : ')
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integer, fractional = val1.split('.')
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val1 = float(val1)
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if int(integer)== 0 and len(fractional) == 2:
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break
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except ValueError:
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pass
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print('ERROR! Use format 0.## for DNA sequence identity threshold.')
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#Input validation for the overlap value.
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while True:
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try:
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val2 =input( 'DNA Sequence Alignment Overlap Value (e.g. 0.67, 0.75)? : ')
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integer, fractional = val2.split('.')
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val2 = float(val2)
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if int(integer)== 0 and len(fractional) == 2:
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break
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except ValueError:
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pass
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print('ERROR! Use format 0.## for DNA sequence alignment overlap value.')
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#Selects DNA fasta files in "to_cluster" folder and clusters them with CD-HIT.
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if not os.path.isdir(args.input):
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for file in tqdm(os.listdir('to_cluster')):
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print(f'Error: Input folder "{args.input}" does not exist.')
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if file.endswith('.fasta'):
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exit(1)
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os.system('cd-hit-est -i to_cluster/' + file + ' -o Clustered/' + file + ' -c %s -d 0 -aS %s' %( val1, val2))
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#Renaming the result of the clustering.
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if not os.path.isdir(args.output):
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for file in os.listdir('Clustered'):
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os.mkdir(args.output)
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if file.endswith('.clstr'):
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os.rename('Clustered/' + file, 'Clustered/' + file.split('FILE')[0] + 'Clustered.txt')
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# Prompts for user input and function call.
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if args.type == 'aa':
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choice_1 = input('Are you clustering Amino Acids or DNA? (AA or DNA) : ')
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threshold = input_validation(args.threshold, 'ERROR! Use format 0.## for Amino acids sequence identity threshold.')
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if choice_1 in ['AA', 'Aa', 'aa']:
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overlap = input_validation(args.overlap, 'ERROR! Use format 0.## for Amino acids sequence alignment overlap value.')
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cluster_AA()
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cluster_sequences('cd-hit', threshold, overlap, args.input, args.output)
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elif choice_1 in ['DNA', 'Dna', 'dna']:
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elif args.type == 'dna':
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cluster_DNA()
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threshold = input_validation(args.threshold, 'ERROR! Use format 0.## for DNA sequence identity threshold.')
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overlap = input_validation(args.overlap, 'ERROR! Use format 0.## for DNA sequence alignment overlap value.')
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cluster_sequences('cd-hit-est', threshold, overlap, args.input, args.output)
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else:
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else:
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print('Sorry. This program can only cluster Amino Acids and DNA')
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print('Invalid sequence type. Choose "aa" for Amino Acids or "dna" for DNA.')
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exit(1)
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cluster()
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if __name__ == "__main__":
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main()
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