File size: 5,134 Bytes
6c23825 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 | #!/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()
|