|
| 1 | +""" |
| 2 | +This module provides functions for parsing and validating command-line arguments for the amplicon_covs script. |
| 3 | +
|
| 4 | +The script requires the following input files: |
| 5 | +- A BED file with primers as given by AmpliGone. |
| 6 | +- A TSV file with coverages as given by TrueConsense. |
| 7 | +- A sample ID. |
| 8 | +- An output TSV file for average coverage per amplicon. |
| 9 | +
|
| 10 | +The module includes the following functions: |
| 11 | +- _common_file_checks: Perform common checks on a file to ensure it exists, is not empty, and is readable. |
| 12 | +- check_primers_file: Validate the primers file to ensure it meets the required criteria. |
| 13 | +- check_coverages_file: Validate the coverages file to ensure it meets the required criteria. |
| 14 | +- check_output_file: Validate the output file to ensure it meets the required criteria. |
| 15 | +- parse_args: Parse and validate command-line arguments for the script. |
| 16 | +
|
| 17 | +Each function raises an ArgumentTypeError if the input does not meet the required criteria. |
| 18 | +
|
| 19 | +Example usage: |
| 20 | +-------------- |
| 21 | +To use this module, import it and call the parse_args function with the appropriate arguments. |
| 22 | +
|
| 23 | + from amplicon_arg_parser import parse_args |
| 24 | +
|
| 25 | + args = parse_args() |
| 26 | + print(args.primers) |
| 27 | + print(args.coverages) |
| 28 | + print(args.key) |
| 29 | + print(args.output) |
| 30 | +""" |
| 31 | + |
| 32 | +import os |
| 33 | +from argparse import ArgumentParser, ArgumentTypeError, Namespace |
| 34 | + |
| 35 | + |
| 36 | +def _common_file_checks(filename: str) -> None: |
| 37 | + """ |
| 38 | + Perform common checks on a file to ensure it exists, is not empty, and is readable. |
| 39 | +
|
| 40 | + This function raises an ArgumentTypeError if any of the following conditions are not met: |
| 41 | + - The file exists. |
| 42 | + - The file is not empty. |
| 43 | + - The file is readable. |
| 44 | +
|
| 45 | + Parameters |
| 46 | + ---------- |
| 47 | + filename : str |
| 48 | + The path to the file to be checked. |
| 49 | +
|
| 50 | + Raises |
| 51 | + ------ |
| 52 | + ArgumentTypeError |
| 53 | + If the file does not exist, is empty, or is not readable. |
| 54 | + """ |
| 55 | + if not os.path.isfile(filename): |
| 56 | + raise ArgumentTypeError(f"File '{filename}' does not exist.") |
| 57 | + |
| 58 | + if os.path.getsize(filename) == 0: |
| 59 | + raise ArgumentTypeError(f"File '{filename}' is empty.") |
| 60 | + |
| 61 | + if not os.access(filename, os.R_OK): |
| 62 | + raise ArgumentTypeError(f"File '{filename}' is not readable.") |
| 63 | + |
| 64 | + |
| 65 | +def check_primers_file(filename: str) -> str: |
| 66 | + """ |
| 67 | + Validate the primers file to ensure it meets the required criteria. |
| 68 | + Does not open the file or check its contents. |
| 69 | +
|
| 70 | + This function performs the following checks: |
| 71 | + - The file exists, is not empty, and is readable (using _common_file_checks). |
| 72 | + - The file has a .bed extension. |
| 73 | +
|
| 74 | + Parameters |
| 75 | + ---------- |
| 76 | + filename : str |
| 77 | + The path to the primers file to be checked. |
| 78 | +
|
| 79 | + Returns |
| 80 | + ------- |
| 81 | + str |
| 82 | + The validated filename. |
| 83 | +
|
| 84 | + Raises |
| 85 | + ------ |
| 86 | + ArgumentTypeError |
| 87 | + If the file does not exist, is empty, is not readable, or does not have a .bed extension. |
| 88 | + """ |
| 89 | + _common_file_checks(filename) |
| 90 | + if not filename.lower().endswith(".bed"): |
| 91 | + raise ArgumentTypeError("Primers file must be a BED file.") |
| 92 | + |
| 93 | + return filename |
| 94 | + |
| 95 | + |
| 96 | +def check_coverages_file(filename: str) -> str: |
| 97 | + """ |
| 98 | + Validate the coverages file to ensure it meets the required criteria. |
| 99 | + Does not open the file or check its contents. |
| 100 | +
|
| 101 | + This function performs the following checks: |
| 102 | + - The file exists, is not empty, and is readable (using _common_file_checks). |
| 103 | + - The file has a .tsv extension. |
| 104 | +
|
| 105 | + Parameters |
| 106 | + ---------- |
| 107 | + filename : str |
| 108 | + The path to the coverages file to be checked. |
| 109 | +
|
| 110 | + Returns |
| 111 | + ------- |
| 112 | + str |
| 113 | + The validated filename. |
| 114 | +
|
| 115 | + Raises |
| 116 | + ------ |
| 117 | + ArgumentTypeError |
| 118 | + If the file does not exist, is empty, is not readable, or does not have a .tsv extension. |
| 119 | + """ |
| 120 | + _common_file_checks(filename) |
| 121 | + |
| 122 | + if not filename.lower().endswith(".tsv"): |
| 123 | + raise ArgumentTypeError("Coverages file must be a TSV file.") |
| 124 | + |
| 125 | + return filename |
| 126 | + |
| 127 | + |
| 128 | +def check_output_file(filename: str) -> str: |
| 129 | + """ |
| 130 | + Validate the output file to ensure it meets the required criteria. |
| 131 | + Does not open the file or check its contents. |
| 132 | +
|
| 133 | + This function performs the following checks: |
| 134 | + - The file has a .csv extension. |
| 135 | + - The file does not already exist. |
| 136 | + - The directory containing the file is writable. |
| 137 | +
|
| 138 | + Parameters |
| 139 | + ---------- |
| 140 | + filename : str |
| 141 | + The path to the output file to be checked. |
| 142 | +
|
| 143 | + Returns |
| 144 | + ------- |
| 145 | + str |
| 146 | + The validated filename. |
| 147 | +
|
| 148 | + Raises |
| 149 | + ------ |
| 150 | + ArgumentTypeError |
| 151 | + If the file does not have a .csv extension, already exists, or the directory is not writable. |
| 152 | + """ |
| 153 | + if not filename.lower().endswith(".csv"): |
| 154 | + raise ArgumentTypeError("Output file must be a CSV file.") |
| 155 | + |
| 156 | + if os.path.isfile(filename): |
| 157 | + raise ArgumentTypeError( |
| 158 | + f"Output file '{filename}' already exists. Please choose another name." |
| 159 | + ) |
| 160 | + |
| 161 | + if not os.access(os.path.dirname(filename), os.W_OK): |
| 162 | + raise ArgumentTypeError( |
| 163 | + f"Directory '{os.path.dirname(filename)}' is not writable." |
| 164 | + ) |
| 165 | + |
| 166 | + return filename |
| 167 | + |
| 168 | + |
| 169 | +def parse_args(args: list[str] | None = None) -> Namespace: |
| 170 | + """ |
| 171 | + Parse command-line arguments for the amplicov_covs script. |
| 172 | +
|
| 173 | + This function sets up the argument parser and defines the required arguments for the script. |
| 174 | + It validates the input files using the specified check functions. |
| 175 | +
|
| 176 | + Parameters |
| 177 | + ---------- |
| 178 | + args : list[str], optional |
| 179 | + A list of command-line arguments to parse. If None, the arguments are taken from sys.argv. |
| 180 | + This parameter is used for testing purposes. |
| 181 | +
|
| 182 | + Returns |
| 183 | + ------- |
| 184 | + Namespace |
| 185 | + An argparse.Namespace object containing the parsed arguments. |
| 186 | +
|
| 187 | + Arguments |
| 188 | + --------- |
| 189 | + --primers : File |
| 190 | + Input BED file with primers as given by AmpliGone. This file is validated by check_primers_file. |
| 191 | +
|
| 192 | + --coverages : File |
| 193 | + Input file with coverages as given by TrueConsense. This file is validated by check_coverages_file. |
| 194 | +
|
| 195 | + --key : String |
| 196 | + Sample ID. |
| 197 | +
|
| 198 | + --output : File |
| 199 | + Output file with average coverage per amplicon. This file is validated by check_output_file. |
| 200 | +
|
| 201 | + Raises |
| 202 | + ------ |
| 203 | + ArgumentTypeError |
| 204 | + If any of the input files do not meet the required criteria. |
| 205 | + """ |
| 206 | + parser = ArgumentParser() |
| 207 | + |
| 208 | + parser.add_argument( |
| 209 | + "--primers", |
| 210 | + metavar="File", |
| 211 | + type=check_primers_file, |
| 212 | + help="input BED file with primers as given by AmpliGone", |
| 213 | + required=True, |
| 214 | + ) |
| 215 | + |
| 216 | + parser.add_argument( |
| 217 | + "--coverages", |
| 218 | + metavar="File", |
| 219 | + type=check_coverages_file, |
| 220 | + help="Input file with coverages as given by TrueConsense", |
| 221 | + required=True, |
| 222 | + ) |
| 223 | + |
| 224 | + parser.add_argument( |
| 225 | + "--key", |
| 226 | + metavar="String", |
| 227 | + type=str, |
| 228 | + help="Sample ID", |
| 229 | + required=True, |
| 230 | + ) |
| 231 | + |
| 232 | + parser.add_argument( |
| 233 | + "--output", |
| 234 | + metavar="File", |
| 235 | + type=check_output_file, |
| 236 | + help="Output file with average coverage per amplicon", |
| 237 | + required=True, |
| 238 | + ) |
| 239 | + |
| 240 | + return parser.parse_args(args) |
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