YuuMJ1997/EukPhylo
1
0
Fork 0
mirror of http://43.156.76.180:8026/YuuMJ/EukPhylo.git synced 2025-12-27 03:40:24 +08:00
Code Issues Packages Projects Releases Wiki Activity

Delete Utilities/for_fastas/Cluster.py

Browse Source
This commit is contained in:
Adri K. Grow 2025-04-06 23:35:47 -04:00 committed by GitHub
parent 0cfea8840c
commit 6a9ae23e8c
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
1 changed files with 0 additions and 67 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

67
Utilities/for_fastas/Cluster.py
View File

@ -1,67 +0,0 @@
'''
#Author, date: Godwin Ani and Laura Katz, 9th- Feb - 2023.
#Dependencies: Python3, CD-Hit
#Intent: For clustering nucleotide or amino acid sequences with the CD-Hit program.
#Inputs: A folder of containing Amino acid or DNA fasta files.
#Outputs: A folder of clustered files.
#Example: python Cluster.py --type dna --identity 0.95 --overlap 0.67 --input input_folder_dna --output output_folder_dna
'''
import os
import argparse
from tqdm import tqdm
import subprocess
def input_validation(value, error_message):
try:
integer, fractional = value.split('.')
value = float(value)
if int(integer) == 0 and len(fractional) == 2:
return value
except ValueError:
pass
print(error_message)
exit(1)
def cluster_sequences(program, identity, overlap, input_folder, output_folder):
for file in tqdm(os.listdir(input_folder)):
if file.endswith('.fasta'):
subprocess.run([f'{program}', '-i', f'{input_folder}/{file}', '-o', f'{output_folder}/{file}', '-c', f'{identity}', '-d', '0', '-aS', f'{overlap}'])
for file in os.listdir(output_folder):
if file.endswith('.clstr'):
os.rename(f'{output_folder}/{file}', f'{output_folder}/{file.split("FILE")[0]}Clustered.txt')
def main():
parser = argparse.ArgumentParser(description='Cluster amino acid or DNA sequences using CD-HIT.')
parser.add_argument('--type', choices=['aa', 'dna'], required=True, help='Type of sequences (aa for Amino Acids, dna for DNA)')
parser.add_argument('--identity', type=str, required=True, help='Sequence Identity Threshold (e.g., 0.99, 0.95)')
parser.add_argument('--overlap', type=str, required=True, help='Sequence Alignment Overlap Value (e.g., 0.67, 0.75)')
parser.add_argument('--input_files', type=str, required=True, help='Input folder containing sequences in fasta format')
parser.add_argument('--output', type=str, required=True, help='Output folder for clustered sequences')
args = parser.parse_args()
if not os.path.isdir(args.input_files):
print(f'Error: Input folder "{args.input_files}" does not exist.')
exit(1)
if not os.path.isdir(args.output):
os.mkdir(args.output)
if args.type == 'aa':
identity = input_validation(args.identity, 'ERROR! Use format 0.## for Amino acids sequence identity threshold.')
overlap = input_validation(args.overlap, 'ERROR! Use format 0.## for Amino acids sequence alignment overlap value.')
cluster_sequences('cd-hit', identity, overlap, args.input_files, args.output)
elif args.type == 'dna':
identity = input_validation(args.identity, 'ERROR! Use format 0.## for DNA sequence identity threshold.')
overlap = input_validation(args.overlap, 'ERROR! Use format 0.## for DNA sequence alignment overlap value.')
cluster_sequences('cd-hit-est', identity, overlap, args.input_files, args.output)
else:
print('Invalid sequence type. Choose "aa" for Amino Acids or "dna" for NTD.')
exit(1)
if __name__ == "__main__":
main()