common
Common CLI options for protein-quest.
BatchSize = PositiveInt
module-attribute
Type for batch size parameters (positive integers > 0).
ConfidenceThreshold = NonNegativeFloat
module-attribute
Type for confidence threshold parameters (non-negative floats >= 0).
InputDir = Annotated[Path, Parameter(validator=(validators.Path(exists=True, file_okay=False))), INPUT_DIR]
module-attribute
Type for input directory parameters (directory paths).
InputFile = Annotated[StdioPath, Parameter(validator=(StdioPathValidator(exists=True, dir_okay=False))), INPUT_FILE]
module-attribute
Type for input file parameters (file paths that can also be "-" for stdin).
Limit = PositiveInt
module-attribute
Type for limit parameters (positive integers > 0).
MaxResidues = PositiveInt
module-attribute
Type for maximum residue parameters (positive integers > 0).
MaxSequenceLength = PositiveInt
module-attribute
Type for maximum sequence length parameters (positive integers > 0).
MinResidues = PositiveInt
module-attribute
Type for minimum residue parameters (positive integers > 0).
MinSequenceLength = PositiveInt
module-attribute
Type for minimum sequence length parameters (positive integers > 0).
OutputDir = Annotated[Path, Parameter(validator=(validators.Path(file_okay=False))), OUTPUT_DIR]
module-attribute
Type for output directory parameters (directory paths).
OutputFile = Annotated[StdioPath, Parameter(validator=(StdioPathValidator(dir_okay=False))), OUTPUT_FILE]
module-attribute
Type for output file parameters (file paths that can also be "-" for stdout).
Timeout = PositiveInt
module-attribute
Type for timeout parameters (positive integers > 0).
CacheParameter
dataclass
Cache-related CLI options.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
no_cache
|
Annotated[bool, Parameter(negative='')]
|
Disable caching of files to central location. |
False
|
cache_dir
|
Path
|
Directory to use as cache for files. |
user_cache_root_dir()
|
copy_method
|
Literal['copy', 'symlink', 'hardlink']
|
How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. |
'hardlink'
|
Common
dataclass
Common CLI options shared across all commands.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
verbose
|
Annotated[int, Parameter(name=(-v, --verbose), count=True)]
|
Increase verbosity (use multiple times for more detail). |
0
|
quiet
|
Annotated[int, Parameter(name=(-q, --quiet), count=True)]
|
Decrease verbosity (use multiple times for less output). |
0
|
prov
|
Annotated[bool, Parameter(negative=''), RECORD_TRIGGER]
|
Whether to write provenance information about the command execution to ro-crate-metadata.json file. |
False
|
__post_init__()
Automatically configure logging when Common instance is created.
StdioPathValidator
Bases: Path
Custom Path validator that allows "-" for stdin/stdout.
This validator checks if the path is "-", and if so, it bypasses Path validation.
If given '-', it also checks if a file named '-' already exists, which would conflict with stdin/stdout usage.
setup_logging(verbose, quiet)
Configure root logging and console quiet mode
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
verbose
|
int
|
Verbosity level |
required |
quiet
|
int
|
Quietness level. |
required |
Raises:
| Type | Description |
|---|---|
ValueError
|
If both verbose and quiet are used together. |
to_cacher(cache_params)
Initialize cacher based on parameters.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
cache_params
|
CacheParameter | None
|
Cache parameters from CLI. |
required |
Returns:
| Type | Description |
|---|---|
Cacher
|
Initialized cacher instance. |