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Acr_Prophage_External_Validation_Dataset / double_diff /batch_run_foldseek.py

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#!/usr/bin/env python3

import argparse
import os
import subprocess
import shlex
from tqdm import tqdm
import multiprocessing
import shutil  # MODIFICATION: Import shutil for directory cleanup

def process_pdb_file(pdb_file, input_dir, output_dir, target_db, tmp_dir, show_compare=False):
    pdb_path = os.path.join(input_dir, pdb_file)
    base_name = os.path.splitext(pdb_file)[0]

    # --- MODIFICATION START: Solve Race Condition ---
    # Create a unique temporary directory for this specific job
    # to avoid conflicts when running in parallel.
    # We use the PDB base name as a unique identifier for the sub-directory.
    job_tmp_dir = os.path.join(tmp_dir, base_name)
    os.makedirs(job_tmp_dir, exist_ok=True)

    if show_compare:
        output_extension = ".html"  # Set extension to .html if show_compare is true
        format_option = "--format-mode 3"
    else:
        output_extension = ".txt"  # Default extension is .txt
        format_option = (
            "--format-output query,target,prob,alntmscore,lddt,fident,alnlen,"
            "mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits"
        )
    
    # Construct the final output path with the correct extension
    output_path = os.path.join(output_dir, f"{base_name}{output_extension}")
    # --- MODIFICATION END ---

    safe_pdb_path = shlex.quote(pdb_path)
    # MODIFICATION: Use the new output_path variable
    safe_output_path = shlex.quote(output_path)
    safe_target_db = shlex.quote(target_db)
    # MODIFICATION: Use the unique job-specific temp directory
    safe_job_tmp_dir = shlex.quote(job_tmp_dir)

    # The format_option is now defined above, so the old if/else is removed
    
    foldseek_cmd = (
        f"foldseek easy-search "
        # MODIFICATION: Use the new safe_output_path and safe_job_tmp_dir variables
        f"{safe_pdb_path} {safe_target_db} {safe_output_path} {safe_job_tmp_dir} "
        f"{format_option}"
    )

    try:
        result = subprocess.run(
            foldseek_cmd,
            shell=True,
            check=True,
            stdout=subprocess.PIPE,
            stderr=subprocess.PIPE,
            text=True
        )
    except subprocess.CalledProcessError as e:
        # MODIFICATION: Clean up even on failure
        shutil.rmtree(job_tmp_dir)
        return f"Warning: Failed to process {pdb_file}: {e.stderr}"
    
    # --- MODIFICATION START: Clean up the unique temp directory ---
    # After the process is successfully finished, remove its unique temp dir
    try:
        shutil.rmtree(job_tmp_dir)
    except OSError as e:
        # Log a warning if cleanup fails, but don't crash
        return f"Warning: Successfully processed {pdb_file} but failed to clean up temp dir {job_tmp_dir}: {e}"
    # --- MODIFICATION END ---

    return f"Successfully processed {pdb_file}"


def main():
    parser = argparse.ArgumentParser(description='Batch processing of Foldseek structure alignment')
    parser.add_argument('-i', '--input', required=True, help='Input directory containing PDB files')
    parser.add_argument('-o', '--output', required=True, help='Output directory for TXT/HTML results') # MODIFICATION: Updated help text
    parser.add_argument('-t', '--target', required=True, help='Target database for Foldseek search')
    parser.add_argument('-T', '--tmp', default='tmp', help='Temporary directory for intermediate files')
    parser.add_argument('-w', '--workers', type=int, default=4, help='Number of worker processes')
    parser.add_argument("--show_compare", action="store_true", help="If set, will output .html files using '--format-mode 3'") # MODIFICATION: Updated help text
    
    args = parser.parse_args()
    
    os.makedirs(args.output, exist_ok=True)
    os.makedirs(args.tmp, exist_ok=True)
    
    pdb_files = [f for f in os.listdir(args.input) if f.endswith('.pdb')]
    
    if not pdb_files:
        print(f"Error: No PDB files found in directory '{args.input}'")
        return

    # MODIFICATION: Use a list to store results for better error logging
    results = []
    
    with tqdm(total=len(pdb_files), desc="Progress") as pbar:
        def update_progress(result):
            # MODIFICATION: Store the result message and update the bar
            results.append(result)
            pbar.update(1)

        with multiprocessing.Pool(processes=args.workers) as pool:
            for pdb_file in pdb_files:
                pool.apply_async(
                    process_pdb_file,
                    (pdb_file, args.input, args.output, args.target, args.tmp, args.show_compare),
                    callback=update_progress,
                    error_callback=lambda e: pbar.update(1) # MODIFICATION: Ensure bar updates on critical error
                )
            pool.close()
            pool.join()
    
    print(f"\nProcessing completed! Results saved to: {args.output}")

    # MODIFICATION: Log any warnings at the end
    warnings = [r for r in results if r.startswith("Warning:")]
    if warnings:
        print("\n--- Warnings ---")
        for w in warnings:
            print(w)


if __name__ == '__main__':
    main()

	#!/usr/bin/env python3

	import argparse
	import os
	import subprocess
	import shlex
	from tqdm import tqdm
	import multiprocessing
	import shutil # MODIFICATION: Import shutil for directory cleanup

	def process_pdb_file(pdb_file, input_dir, output_dir, target_db, tmp_dir, show_compare=False):
	pdb_path = os.path.join(input_dir, pdb_file)
	base_name = os.path.splitext(pdb_file)[0]

	# --- MODIFICATION START: Solve Race Condition ---
	# Create a unique temporary directory for this specific job
	# to avoid conflicts when running in parallel.
	# We use the PDB base name as a unique identifier for the sub-directory.
	job_tmp_dir = os.path.join(tmp_dir, base_name)
	os.makedirs(job_tmp_dir, exist_ok=True)

	if show_compare:
	output_extension = ".html" # Set extension to .html if show_compare is true
	format_option = "--format-mode 3"
	else:
	output_extension = ".txt" # Default extension is .txt
	format_option = (
	"--format-output query,target,prob,alntmscore,lddt,fident,alnlen,"
	"mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits"
	)

	# Construct the final output path with the correct extension
	output_path = os.path.join(output_dir, f"{base_name}{output_extension}")
	# --- MODIFICATION END ---

	safe_pdb_path = shlex.quote(pdb_path)
	# MODIFICATION: Use the new output_path variable
	safe_output_path = shlex.quote(output_path)
	safe_target_db = shlex.quote(target_db)
	# MODIFICATION: Use the unique job-specific temp directory
	safe_job_tmp_dir = shlex.quote(job_tmp_dir)

	# The format_option is now defined above, so the old if/else is removed

	foldseek_cmd = (
	f"foldseek easy-search "
	# MODIFICATION: Use the new safe_output_path and safe_job_tmp_dir variables
	f"{safe_pdb_path} {safe_target_db} {safe_output_path} {safe_job_tmp_dir} "
	f"{format_option}"
	)

	try:
	result = subprocess.run(
	foldseek_cmd,
	shell=True,
	check=True,
	stdout=subprocess.PIPE,
	stderr=subprocess.PIPE,
	text=True
	)
	except subprocess.CalledProcessError as e:
	# MODIFICATION: Clean up even on failure
	shutil.rmtree(job_tmp_dir)
	return f"Warning: Failed to process {pdb_file}: {e.stderr}"

	# --- MODIFICATION START: Clean up the unique temp directory ---
	# After the process is successfully finished, remove its unique temp dir
	try:
	shutil.rmtree(job_tmp_dir)
	except OSError as e:
	# Log a warning if cleanup fails, but don't crash
	return f"Warning: Successfully processed {pdb_file} but failed to clean up temp dir {job_tmp_dir}: {e}"
	# --- MODIFICATION END ---

	return f"Successfully processed {pdb_file}"


	def main():
	parser = argparse.ArgumentParser(description='Batch processing of Foldseek structure alignment')
	parser.add_argument('-i', '--input', required=True, help='Input directory containing PDB files')
	parser.add_argument('-o', '--output', required=True, help='Output directory for TXT/HTML results') # MODIFICATION: Updated help text
	parser.add_argument('-t', '--target', required=True, help='Target database for Foldseek search')
	parser.add_argument('-T', '--tmp', default='tmp', help='Temporary directory for intermediate files')
	parser.add_argument('-w', '--workers', type=int, default=4, help='Number of worker processes')
	parser.add_argument("--show_compare", action="store_true", help="If set, will output .html files using '--format-mode 3'") # MODIFICATION: Updated help text

	args = parser.parse_args()

	os.makedirs(args.output, exist_ok=True)
	os.makedirs(args.tmp, exist_ok=True)

	pdb_files = [f for f in os.listdir(args.input) if f.endswith('.pdb')]

	if not pdb_files:
	print(f"Error: No PDB files found in directory '{args.input}'")
	return

	# MODIFICATION: Use a list to store results for better error logging
	results = []

	with tqdm(total=len(pdb_files), desc="Progress") as pbar:
	def update_progress(result):
	# MODIFICATION: Store the result message and update the bar
	results.append(result)
	pbar.update(1)

	with multiprocessing.Pool(processes=args.workers) as pool:
	for pdb_file in pdb_files:
	pool.apply_async(
	process_pdb_file,
	(pdb_file, args.input, args.output, args.target, args.tmp, args.show_compare),
	callback=update_progress,
	error_callback=lambda e: pbar.update(1) # MODIFICATION: Ensure bar updates on critical error
	)
	pool.close()
	pool.join()

	print(f"\nProcessing completed! Results saved to: {args.output}")

	# MODIFICATION: Log any warnings at the end
	warnings = [r for r in results if r.startswith("Warning:")]
	if warnings:
	print("\n--- Warnings ---")
	for w in warnings:
	print(w)


	if __name__ == '__main__':
	main()