Merge pull request #109 from RIVM-bioinformatics/IDSBIO-472-refactor-amplicon-covs

refactor: amplicon_covs.py

Author: florianzwagemaker

ViroConstrictor/workflow/scripts/__init__.py

@@ -0,0 +1,240 @@
+"""
+This module provides functions for parsing and validating command-line arguments for the amplicon_covs script.
+
+The script requires the following input files:
+- A BED file with primers as given by AmpliGone.
+- A TSV file with coverages as given by TrueConsense.
+- A sample ID.
+- An output TSV file for average coverage per amplicon.
+
+The module includes the following functions:
+- _common_file_checks: Perform common checks on a file to ensure it exists, is not empty, and is readable.
+- check_primers_file: Validate the primers file to ensure it meets the required criteria.
+- check_coverages_file: Validate the coverages file to ensure it meets the required criteria.
+- check_output_file: Validate the output file to ensure it meets the required criteria.
+- parse_args: Parse and validate command-line arguments for the script.
+
+Each function raises an ArgumentTypeError if the input does not meet the required criteria.
+
+Example usage:
+--------------
+To use this module, import it and call the parse_args function with the appropriate arguments.
+
+    from amplicon_arg_parser import parse_args
+
+    args = parse_args()
+    print(args.primers)
+    print(args.coverages)
+    print(args.key)
+    print(args.output)
+"""
+
+import os
+from argparse import ArgumentParser, ArgumentTypeError, Namespace
+
+
+def _common_file_checks(filename: str) -> None:
+    """
+    Perform common checks on a file to ensure it exists, is not empty, and is readable.
+
+    This function raises an ArgumentTypeError if any of the following conditions are not met:
+    - The file exists.
+    - The file is not empty.
+    - The file is readable.
+
+    Parameters
+    ----------
+    filename : str
+        The path to the file to be checked.
+
+    Raises
+    ------
+    ArgumentTypeError
+        If the file does not exist, is empty, or is not readable.
+    """
+    if not os.path.isfile(filename):
+        raise ArgumentTypeError(f"File '{filename}' does not exist.")
+
+    if os.path.getsize(filename) == 0:
+        raise ArgumentTypeError(f"File '{filename}' is empty.")
+
+    if not os.access(filename, os.R_OK):
+        raise ArgumentTypeError(f"File '{filename}' is not readable.")
+
+
+def check_primers_file(filename: str) -> str:
+    """
+    Validate the primers file to ensure it meets the required criteria.
+    Does not open the file or check its contents.
+
+    This function performs the following checks:
+    - The file exists, is not empty, and is readable (using _common_file_checks).
+    - The file has a .bed extension.
+
+    Parameters
+    ----------
+    filename : str
+        The path to the primers file to be checked.
+
+    Returns
+    -------
+    str
+        The validated filename.
+
+    Raises
+    ------
+    ArgumentTypeError
+        If the file does not exist, is empty, is not readable, or does not have a .bed extension.
+    """
+    _common_file_checks(filename)
+    if not filename.lower().endswith(".bed"):
+        raise ArgumentTypeError("Primers file must be a BED file.")
+
+    return filename
+
+
+def check_coverages_file(filename: str) -> str:
+    """
+    Validate the coverages file to ensure it meets the required criteria.
+    Does not open the file or check its contents.
+
+    This function performs the following checks:
+    - The file exists, is not empty, and is readable (using _common_file_checks).
+    - The file has a .tsv extension.
+
+    Parameters
+    ----------
+    filename : str
+        The path to the coverages file to be checked.
+
+    Returns
+    -------
+    str
+        The validated filename.
+
+    Raises
+    ------
+    ArgumentTypeError
+        If the file does not exist, is empty, is not readable, or does not have a .tsv extension.
+    """
+    _common_file_checks(filename)
+
+    if not filename.lower().endswith(".tsv"):
+        raise ArgumentTypeError("Coverages file must be a TSV file.")
+
+    return filename
+
+
+def check_output_file(filename: str) -> str:
+    """
+    Validate the output file to ensure it meets the required criteria.
+    Does not open the file or check its contents.
+
+    This function performs the following checks:
+    - The file has a .csv extension.
+    - The file does not already exist.
+    - The directory containing the file is writable.
+
+    Parameters
+    ----------
+    filename : str
+        The path to the output file to be checked.
+
+    Returns
+    -------
+    str
+        The validated filename.
+
+    Raises
+    ------
+    ArgumentTypeError
+        If the file does not have a .csv extension, already exists, or the directory is not writable.
+    """
+    if not filename.lower().endswith(".csv"):
+        raise ArgumentTypeError("Output file must be a CSV file.")
+
+    if os.path.isfile(filename):
+        raise ArgumentTypeError(
+            f"Output file '{filename}' already exists. Please choose another name."
+        )
+
+    if not os.access(os.path.dirname(filename), os.W_OK):
+        raise ArgumentTypeError(
+            f"Directory '{os.path.dirname(filename)}' is not writable."
+        )
+
+    return filename
+
+
+def parse_args(args: list[str] | None = None) -> Namespace:
+    """
+    Parse command-line arguments for the amplicov_covs script.
+
+    This function sets up the argument parser and defines the required arguments for the script.
+    It validates the input files using the specified check functions.
+
+    Parameters
+    ----------
+    args : list[str], optional
+        A list of command-line arguments to parse. If None, the arguments are taken from sys.argv.
+        This parameter is used for testing purposes.
+
+    Returns
+    -------
+    Namespace
+        An argparse.Namespace object containing the parsed arguments.
+
+    Arguments
+    ---------
+    --primers : File
+        Input BED file with primers as given by AmpliGone. This file is validated by check_primers_file.
+
+    --coverages : File
+        Input file with coverages as given by TrueConsense. This file is validated by check_coverages_file.
+
+    --key : String
+        Sample ID.
+
+    --output : File
+        Output file with average coverage per amplicon. This file is validated by check_output_file.
+
+    Raises
+    ------
+    ArgumentTypeError
+        If any of the input files do not meet the required criteria.
+    """
+    parser = ArgumentParser()
+
+    parser.add_argument(
+        "--primers",
+        metavar="File",
+        type=check_primers_file,
+        help="input BED file with primers as given by AmpliGone",
+        required=True,
+    )
+
+    parser.add_argument(
+        "--coverages",
+        metavar="File",
+        type=check_coverages_file,
+        help="Input file with coverages as given by TrueConsense",
+        required=True,
+    )
+
+    parser.add_argument(
+        "--key",
+        metavar="String",
+        type=str,
+        help="Sample ID",
+        required=True,
+    )
+
+    parser.add_argument(
+        "--output",
+        metavar="File",
+        type=check_output_file,
+        help="Output file with average coverage per amplicon",
+        required=True,
+    )
+
+    return parser.parse_args(args)