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74 lines
3.6 KiB
Python
74 lines
3.6 KiB
Python
'''
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#Author, date: Godwin Ani and Laura Katz, Feb 9th 2023
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#Modified: Adri Grow, April 6th 2025 to allow clustering at 100% (1.0) and output renamed file(s) with id clustered appended to file name
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#Dependencies: Python3, CD-Hit
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#Intent: For clustering nucleotide or amino acid sequences with the CD-Hit program
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#Inputs: A folder of containing AA or DNA fasta files
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#Outputs: A folder of clustered files
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#Example: python Cluster.py -t dna -id 0.95 -ov 0.67 -i input_folder_dna -o output_folder_dna
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'''
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import os
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import argparse
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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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try:
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value = float(value)
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if value == 1.0:
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return value
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integer, fractional = str(value).split('.')
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if int(integer) == 0 and len(fractional) == 2:
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return value
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except ValueError:
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pass
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print(error_message)
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exit(1)
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def cluster_sequences(program, identity, overlap, input_folder, output_folder):
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for file in tqdm(os.listdir(input_folder)):
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if file.endswith('.fasta'):
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output_name = f"{os.path.splitext(file)[0]}_{int(float(identity) * 100)}clustered.fasta"
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subprocess.run([f'{program}', '-i', f'{input_folder}/{file}', '-o', f'{output_folder}/{output_name}', '-c', f'{identity}', '-d', '0', '-aS', f'{overlap}'])
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for file in os.listdir(output_folder):
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if file.endswith('.clstr'):
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base_name = os.path.splitext(file)[0] # removes .clstr
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if base_name.endswith('.fasta'):
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base_name = base_name[:-6] # removes .fasta from end
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new_name = f"{base_name}.txt"
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os.rename(f'{output_folder}/{file}', f'{output_folder}/{new_name}')
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def main():
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parser = argparse.ArgumentParser(description='Cluster amino acid or nucleotide sequences using CD-HIT.')
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parser.add_argument('-t', '--type', choices=['aa', 'dna'], required=True, help='Type of sequences (aa for amino acid, dna for nucleotide)')
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parser.add_argument('-id','--identity', type=str, required=True, help='Sequence identity threshold (e.g. 1.0, 0.99, 0.95)')
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parser.add_argument('-ov', '--overlap', type=str, required=True, help='Sequence alignment overlap value (e.g. 0.67, 0.75)')
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parser.add_argument('-i', '--input_files', type=str, required=True, help='Input folder containing sequences in fasta format')
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parser.add_argument('-o', '--output', type=str, required=True, help='Output folder for clustered sequences ending with -id value')
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args = parser.parse_args()
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if not os.path.isdir(args.input_files):
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print(f'Error: Input folder "{args.input_files}" does not exist.')
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exit(1)
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if not os.path.isdir(args.output):
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os.mkdir(args.output)
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if args.type == 'aa':
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identity = input_validation(args.identity, 'ERROR! Use format 0.## or 1.0 for amino acid sequence identity threshold.')
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overlap = input_validation(args.overlap, 'ERROR! Use format 0.## for amino acid sequence alignment overlap value.')
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cluster_sequences('cd-hit', identity, overlap, args.input_files, args.output)
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elif args.type == 'dna':
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identity = input_validation(args.identity, 'ERROR! Use format 0.## or 1.0 for nucleotide sequence identity threshold.')
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overlap = input_validation(args.overlap, 'ERROR! Use format 0.## for nucleotide sequence alignment overlap value.')
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cluster_sequences('cd-hit-est', identity, overlap, args.input_files, args.output)
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else:
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print('Invalid sequence type. Choose "aa" for amino acids or "dna" for nucleotides.')
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exit(1)
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if __name__ == "__main__":
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main()
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