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nextclade

Module to fetch Nextclade data.

get(id, dir='', version='')

Download specified Nextclade dataset into target directory.

Parameters:

  • id (str) –

    Name of the Nextclade dataset.

  • dir (str, default: '' ) –

    Directory where dataset will be downloaded.

Returns:

  • None –
Source code in src/vargram/data/nextclade.py 
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def get(id, dir='', version=''):
    """Download specified Nextclade dataset into target directory.

    Parameters
    ----------
    id : str 
        Name of the Nextclade dataset.
    dir : str
        Directory where dataset will be downloaded.

    Returns
    -------
    None

    """

    # Define target directory where data will be downloaded
    if isinstance(dir, str) and dir.strip(): # Use user-provided directory 
        target_dir = dir 
        if not os.path.isdir(target_dir):
            os.makedirs(target_dir)
    else: # Or use current working directory by default
        target_dir = os.getcwd()

    get_command = f"nextclade dataset get --name {id} --output-dir {target_dir}"
    if version != '':
        get_command = get_command + f" --tag {version}"
    run_nextclade(get_command.split())

list(full=False)

List available Nextclade datasets.

Parameters:

  • full (bool, default:False, default: False ) –

    Determines if only names of datasets will be shown.

Returns:

  • None –
Source code in src/vargram/data/nextclade.py 
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def list(full=False):
    """List available Nextclade datasets.

    Parameters
    ----------
    full : bool, default:False
        Determines if only names of datasets will be shown.

    Returns
    -------
    None

    """

    if full:
        list_command = "nextclade dataset list"
    else:
        list_command = "nextclade dataset list --only-names"
    run_nextclade(list_command.split(), write=True)

run_nextclade(command, write=False)

Run Nextclade CLI.

Parameters:

  • command (list) –

    Directory where test data will be downloaded.

  • write (bool, default:False, default: False ) –

    Determines whether to print output of command.

Returns:

  • None –
Source code in src/vargram/data/nextclade.py 
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def run_nextclade(command,  write=False):
    """Run Nextclade CLI.

    Parameters
    ----------
    command : list 
        Directory where test data will be downloaded.
    write : bool, default:False
        Determines whether to print output of command.

    Returns
    -------
    None

    """

    try:
        result = subprocess.run(command, check=True, capture_output=True, text=True)
        if write:
            print(result.stdout)
    except subprocess.CalledProcessError as e:
        print(f"Error running Nextclade: {e}")
    except FileNotFoundError:
        print("Nextclade executable not found. Make sure it is included in the system $PATH.")
    except Exception as e:
        print(f"An unexpected error occurred: {e}")