mmcif_validator.py

"""
mmcif_validator.py

Description: This script can validate an mmCIF file using the latest mmCIF dictionary.

"""
__author__ = 'Amudha Kumari Duraisamy'
__email__ = 'emdbhelp@ebi.ac.uk'
__date__ = '2024-11-20'

import os
import subprocess
import argparse
import urllib.request

def parse_arguments():
    """
    Parses command-line arguments for mmCIF file validation.

    Example usage:
        python mmcif_validator.py -c test_data/TOMO_data.cif -d no

    Requirements:
        - Gemmi: A Python package for working with mmCIF files.
        To install:
            pip install gemmi

    Returns:
        argparse.Namespace: Parsed arguments with input CIF file, dictionary file, and output file paths.
    """
    parser = argparse.ArgumentParser(description="Validate a mmCIF file against a mmCIF dictionary.")
    parser.add_argument("-c", "--input_cif_file", required=True, help="Path to the input mmCIF file to validate.")
    parser.add_argument("-d", "--download_dict", choices=["yes", "no"], default="yes",
                        help="Download the latest mmCIF dictionary for validation (default: yes)")
    return parser.parse_args()

def mmcif_validation(cif_file, download_dict, output_file):
    """
    Validates an mmCIF file using the Gemmi validate command and saves the output to a file.

    Parameters:
        cif_file (str): Path to the mmCIF file.
        dic_file (str): Path to the dictionary file for validation.
        output_file (str): Path to save the validation output.

    Returns:
        tuple: (bool, str)
            - bool: True if validation succeeded, False otherwise.
            - str: Message detailing validation results or errors.
    """
    dic_file = "mmcif_tools/mmcif_pdbx_v50.dic"
    if download_dict == "yes":
        urllib.request.urlretrieve("https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic", dic_file)
    try:
        # Ensure input files exist
        if not os.path.isfile(cif_file):
            return False, f"Error: Input CIF file '{cif_file}' does not exist."
        if not os.path.isfile(dic_file):
            return False, f"Error: Dictionary file '{dic_file}' does not exist. Download it using the option -d yes"

        # Construct the Gemmi command
        command = [
            "gemmi", "validate", "-v", cif_file, "-d", dic_file
        ]

        # Execute the command and redirect output to a file
        with open(output_file, "w") as outfile:
            result = subprocess.run(command, stdout=outfile, stderr=subprocess.PIPE, text=True, env=os.environ.copy())

        # Check for errors in stderr or non-zero exit status
        if result.returncode != 0:
            print( f"Validation failed with error and output saved to {output_file}")
            return False
        if result.stderr.strip():
            print(f"Validation encountered issues: {result.stderr.strip()}")
            return False

        print(f"Validation succeeded. Results saved to {output_file}")
        return True

    except Exception as e:
        return False, f"An unexpected error occurred: {str(e)}"

def validate_and_print(input_cif_file, download_dict,  output_val_file):
    """
    A callable function for validation with direct input of arguments.

    Parameters:
        input_cif_file (str): Path to the input mmCIF file.
        cif_dict (str): Path to the mmCIF dictionary file.
        output_val_file (str): Path to save the validation output.
    """
    mmcif_validation(input_cif_file, download_dict, output_val_file)

def main():
    """
    Parses arguments, performs validation, and outputs results.
    """
    args = parse_arguments()
    output_val_file = args.input_cif_file.split(".")[0] + '_val.txt'
    validate_and_print(args.input_cif_file, args.download_dict, output_val_file)

if __name__ == "__main__":
    main()