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Clui

Interface for command-line script.

main()

Main driver.

Source code in snailz/clui.py 
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def main():
    '''Main driver.'''
    parser = argparse.ArgumentParser()
    parser.add_argument('--version', action='store_true', help='show version')
    subparsers = parser.add_subparsers()
    for sub in (
            _assays_parser,
            _db_parser,
            _everything_parser,
            _genomes_parser,
            _grid_parser,
            _mangle_parser,
            _params_parser,
            _plates_parser,
            _samples_parser,
            _staff_parser,
            _surveymap_parser,
    ):
        sub(subparsers)
    options = parser.parse_args()
    if options.version:
        print(importlib.metadata.version('snailz'))
    else:
        options.func(options)

everything(options)

Build everything using default values.

Parameters:

Name Type Description Default
options Namespace

controlling options.

 required
  • paramsdir: input parameters directory.
  • datadir: output data directory.
Source code in snailz/clui.py 
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def everything(options: argparse.Namespace) -> None:
    '''Build everything using default values.

    Args:
        options: controlling options.

    -   paramsdir: input parameters directory.
    -   datadir: output data directory.
    '''
    # Common values
    assays_data = Path(options.datadir, 'assays.json')
    assays_params = Path(options.paramsdir, 'assays.json')
    db_file = Path(options.datadir, 'lab.db')
    designs_data_dir = Path(options.datadir, 'designs')
    genomes_data = Path(options.datadir, 'genomes.json')
    genomes_params = Path(options.paramsdir, 'genomes.json')
    grids_data_dir = Path(options.datadir, 'grids')
    grids_params = Path(options.paramsdir, 'grids.json')
    mangled_data_dir = Path(options.datadir, 'mangled')
    readings_data_dir = Path(options.datadir, 'readings')
    samples_data = Path(options.datadir, 'samples.csv')
    samples_params = Path(options.paramsdir, 'samples.json')
    sites_params = Path(options.paramsdir, 'sites.csv')
    staff_data = Path(options.datadir, 'staff.csv')
    staff_params = Path(options.paramsdir, 'staff.json')
    surveys_params = Path(options.paramsdir, 'surveys.csv')
    surveymap_file = Path(options.datadir, 'survey.png')

    # Ensure root data directory exists
    _verbose(options, 'data directory')
    Path(options.datadir).mkdir(exist_ok=True)

    # Grids
    _verbose(options, 'grids')
    grids_data_dir.mkdir(exist_ok=True)
    grid(_make_options(
        outdir=grids_data_dir,
        params=grids_params,
        sites=sites_params,
    ))

    # Genomes
    _verbose(options, 'genomes')
    genomes(_make_options(
        params=genomes_params,
        outfile=genomes_data,
    ))

    # Samples
    _verbose(options, 'samples')
    samples(_make_options(
        genomes=genomes_data,
        grids=grids_data_dir,
        outfile=samples_data,
        params=samples_params,
        sites=sites_params,
        surveys=surveys_params,
    ))

    # Staff
    _verbose(options, 'staff')
    staff(_make_options(
        params=staff_params,
        outfile=staff_data,
    ))

    # Assays
    _verbose(options, 'assays')
    assays(_make_options(
        genomes=genomes_data,
        outfile=assays_data,
        params=assays_params,
        samples=samples_data,
        staff=staff_data,
    ))

    # Plates
    _verbose(options, 'plates')
    designs_data_dir.mkdir(exist_ok=True)
    readings_data_dir.mkdir(exist_ok=True)
    plates(_make_options(
        designs=designs_data_dir,
        readings=readings_data_dir,
        assays=assays_data,
        params=assays_params,
    ))

    # Database
    _verbose(options, 'db')
    db(_make_options(
        dbfile=db_file,
        assays=assays_data,
        samples=samples_data,
        sites=sites_params,
        staff=staff_data,
        surveys=surveys_params,
    ))

    # Mangled plate files
    _verbose(options, 'mangled')
    mangled_data_dir.mkdir(exist_ok=True)
    mangle(_make_options(
        dbfile=db_file,
        tidy=readings_data_dir,
        outdir=mangled_data_dir,
    ))

    # Survey map
    if options.withmap:
        _verbose(options, 'survey map')
        surveymap(_make_options(
            outfile=surveymap_file,
            samples=samples_data,
        ))

_assays_parser(subparsers)

Add sub-parser for assays.

Source code in snailz/clui.py 
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def _assays_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for assays.'''
    parser = subparsers.add_parser('assays', help='construct assays')
    parser.add_argument('--genomes', type=str, required=True, help='genome file')
    parser.add_argument('--outfile', type=str, default=None, help='output file')
    parser.add_argument('--params', type=str, required=True, help='parameter file')
    parser.add_argument('--samples', type=str, required=True, help='samples file')
    parser.add_argument('--staff', type=str, required=True, help='staff file')
    parser.set_defaults(func=assays)

_db_parser(subparsers)

Add sub-parser for database creation.

Source code in snailz/clui.py 
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def _db_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for database creation.'''
    parser = subparsers.add_parser('db', help='construct database')
    parser.add_argument('--assays', type=str, required=True, help='assay data file')
    parser.add_argument('--dbfile', type=str, required=True, help='output database file')
    parser.add_argument('--samples', type=str, required=True, help='samples data file')
    parser.add_argument('--sites', type=str, required=True, help='sites parameter file')
    parser.add_argument('--surveys', type=str, required=True, help='surveys parameter file')
    parser.set_defaults(func=db)

_everything_parser(subparsers)

Add sub-parser for creating everything.

Source code in snailz/clui.py 
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def _everything_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for creating everything.'''
    parser = subparsers.add_parser('everything', help='build everything with defaults')
    parser.add_argument('--datadir', type=str, required=True, help='output data directory')
    parser.add_argument('--paramsdir', type=str, required=True, help='input parameters directory')
    parser.add_argument('--withmap', action='store_true', help='also generate map')
    parser.add_argument('--verbose', action='store_true', help='report progress')
    parser.set_defaults(func=everything)

_genomes_parser(subparsers)

Add sub-parser for creating genomes.

Source code in snailz/clui.py 
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def _genomes_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for creating genomes.'''
    parser = subparsers.add_parser('genomes', help='construct genomes')
    parser.add_argument('--outfile', type=str, default=None, help='output file')
    parser.add_argument('--params', type=str, required=True, help='parameter file')
    parser.set_defaults(func=genomes)

_grid_parser(subparsers)

Add sub-parser for creating grids.

Source code in snailz/clui.py 
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def _grid_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for creating grids.'''
    parser = subparsers.add_parser('grid', help='construct survey grid')
    parser.add_argument('--outdir', type=str, required=True, help='output directory')
    parser.add_argument('--params', type=str, required=True, help='grid parameter file')
    parser.add_argument('--sites', type=str, required=True, help='site parameter file')
    parser.set_defaults(func=grid)

_mangle_parser(subparsers)

Add sub-parser for mangling plate readings files.

Source code in snailz/clui.py 
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def _mangle_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for mangling plate readings files.'''
    parser = subparsers.add_parser('mangle', help='mangle readings files')
    parser.add_argument('--dbfile', type=str, required=True, help='database file')
    parser.add_argument('--outdir', type=str, required=True, help='output directory')
    parser.add_argument('--tidy', type=str, required=True, help='input directory')
    parser.set_defaults(func=mangle)

_params_parser(subparsers)

Add sub-parser for copying parameters from installed package.

Source code in snailz/clui.py 
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def _params_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for copying parameters from installed package.'''
    parser = subparsers.add_parser('params', help='export parameter files')
    parser.add_argument('--outdir', type=str, required=True, help='output directory')
    parser.set_defaults(func=export_params)

_plates_parser(subparsers)

Add sub-parser for generating plates.

Source code in snailz/clui.py 
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def _plates_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for generating plates.'''
    parser = subparsers.add_parser('plates', help='construct plates')
    parser.add_argument('--assays', type=str, required=True, help='assays file')
    parser.add_argument('--designs', type=str, required=True, help='designs directory')
    parser.add_argument('--params', type=str, required=True, help='parameter file')
    parser.add_argument('--readings', type=str, required=True, help='readings directory')
    parser.set_defaults(func=plates)

_samples_parser(subparsers)

Add sub-parser for generating samples.

Source code in snailz/clui.py 
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def _samples_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for generating samples.'''
    parser = subparsers.add_parser('samples', help='construct samples')
    parser.add_argument('--genomes', type=str, required=True, help='genome file')
    parser.add_argument('--grids', type=str, required=True, help='grids directory')
    parser.add_argument('--outfile', type=str, help='output file')
    parser.add_argument('--params', type=str, required=True, help='parameter file')
    parser.add_argument('--sites', type=str, required=True, help='sites parameter file')
    parser.add_argument('--surveys', type=str, required=True, help='surveys parameter file')
    parser.set_defaults(func=samples)

_staff_parser(subparsers)

Add sub-parser for generating staff.

Source code in snailz/clui.py 
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def _staff_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for generating staff.'''
    parser = subparsers.add_parser('staff', help='construct staff names and IDs')
    parser.add_argument('--params', type=str, required=True, help='parameter file')
    parser.add_argument('--outfile', type=str, required=True, help='output file name')
    parser.set_defaults(func=staff)

_surveymap_parser(subparsers)

Add sub-parser for generating map of survey sites.

Source code in snailz/clui.py 
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def _surveymap_parser(subparsers: argparse._SubParsersAction) -> None:
    '''Add sub-parser for generating map of survey sites.'''
    parser = subparsers.add_parser('surveymap', help='construct survey locations')
    parser.add_argument('--outfile', type=str, required=True, help='output file name')
    parser.add_argument('--samples', type=str, required=True, help='samples data file')
    parser.set_defaults(func=surveymap)

_make_options(**kwargs)

Build an argparse options object.

Parameters:

Name Type Description Default
kwargs dict

fields and values in options object.

 {}

Returns:

Type Description
Namespace

Options object.
Source code in snailz/clui.py 
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def _make_options(**kwargs: dict) -> argparse.Namespace:
    '''Build an argparse options object.

    Args:
        kwargs: fields and values in options object.

    Returns:
        Options object.
    '''
    options = argparse.Namespace()
    for key, value in kwargs.items():
        setattr(options, key, value)
    return options

_verbose(options, msg)

Possibly report progress.

Parameters:

Name Type Description Default
options Namespace

controlling options (must have verbose field).

 required
msg str

what to (possibly) print.

 required
Source code in snailz/clui.py 
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def _verbose(options: argparse.Namespace, msg: str) -> None:
    '''Possibly report progress.

    Args:
        options: controlling options (must have `verbose` field).
        msg: what to (possibly) print.
    '''
    if options.verbose:
        print(f'...{msg}')