Package `read5`

Expand source code

from . import _version
__version__ = _version.get_versions()['version']

from read5.Reader import read

__all__ = [
    "read"
]

Sub-modules

read5.AbstractFileReader
read5.Exceptions
read5.Fast5Reader
read5.Pod5Reader
read5.Reader
read5.Slow5Reader

Functions

def read(filepath: str)

Autodetect file format using extension. Raises UnknownFormatException if format is unknown.

Returns

FileReader: FileReader object of the detected file format

Expand source code

def read(filepath : str):
    '''
    Autodetect file format using extension.
    Raises UnknownFormatException if format is unknown.

    Returns
    -------
    FileReader
        FileReader object of the detected file format
    '''
    if filepath.lower().endswith('.fast5'):
        return Fast5Reader(filepath)
    elif filepath.lower().endswith('.slow5') or filepath.lower().endswith('.blow5'):
        return Slow5Reader(filepath=filepath)
    elif filepath.lower().endswith('.pod5'):
        return Pod5Reader(filepath)
    else:
        raise UnknownFileFormatException(f'Unknown file format: {filepath.split(".")[-1]}')