BioSequenceDataset

BioSequenceDataset loads and saves data to a sequence file.

kedro_datasets.biosequence.BioSequenceDataset

BioSequenceDataset(
    *,
    filepath,
    load_args=None,
    save_args=None,
    credentials=None,
    fs_args=None,
    metadata=None
)

Bases: AbstractDataset[list, list]

BioSequenceDataset loads and saves data to a sequence file.

Examples:

Using the Python API:

>>> from Bio import SeqIO
>>> from io import StringIO
>>> from kedro_datasets.biosequence import BioSequenceDataset
>>>
>>> data = ">Alpha\nACCGGATGTA\n>Beta\nAGGCTCGGTTA\n"
>>> raw_data = []
>>> for record in SeqIO.parse(StringIO(data), "fasta"):
...     raw_data.append(record)
...
>>>
>>> dataset = BioSequenceDataset(
...     filepath=tmp_path / "ls_orchid.fasta",
...     load_args={"format": "fasta"},
...     save_args={"format": "fasta"},
... )
>>> dataset.save(raw_data)
>>> sequence_list = dataset.load()
>>> assert raw_data[0].id == sequence_list[0].id
>>> assert raw_data[0].seq == sequence_list[0].seq

Parameters:

• filepath (str) –

  Filepath in POSIX format to sequence file prefixed with a protocol like s3://. If prefix is not provided, file protocol (local filesystem) will be used. The prefix should be any protocol supported by fsspec.

• load_args (dict[str, Any] | None, default: None ) –

  Options for parsing sequence files by Biopython SeqIO.parse().

• save_args (dict[str, Any] | None, default: None ) –

  file format supported by Biopython SeqIO.write(). E.g. {"format": "fasta"}.

• credentials (dict[str, Any] | None, default: None ) –

  Credentials required to get access to the underlying filesystem. E.g. for GCSFileSystem it should look like {"token": None}.

• fs_args (dict[str, Any] | None, default: None ) –

  Extra arguments to pass into underlying filesystem class constructor (e.g. {"project": "my-project"} for GCSFileSystem), as well as to pass to the filesystem's open method through nested keys open_args_load and open_args_save. Here you can find all available arguments for open: https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.spec.AbstractFileSystem.open All defaults are preserved, except mode, which is set to r when loading and to w when saving.

• metadata (dict[str, Any] | None, default: None ) –

  Any arbitrary metadata. This is ignored by Kedro, but may be consumed by users or external plugins.

Note: Here you can find all supported file formats: https://biopython.org/wiki/SeqIO

Source code in kedro_datasets/biosequence/biosequence_dataset.py

def __init__(  # noqa: PLR0913
    self,
    *,
    filepath: str,
    load_args: dict[str, Any] | None = None,
    save_args: dict[str, Any] | None = None,
    credentials: dict[str, Any] | None = None,
    fs_args: dict[str, Any] | None = None,
    metadata: dict[str, Any] | None = None,
) -> None:
    """
    Creates a new instance of ``BioSequenceDataset`` pointing
    to a concrete filepath.

    Args:
        filepath: Filepath in POSIX format to sequence file prefixed with a protocol like
            `s3://`. If prefix is not provided, `file` protocol (local filesystem) will be used.
            The prefix should be any protocol supported by ``fsspec``.
        load_args: Options for parsing sequence files by Biopython ``SeqIO.parse()``.
        save_args: file format supported by Biopython ``SeqIO.write()``.
            E.g. `{"format": "fasta"}`.
        credentials: Credentials required to get access to the underlying filesystem.
            E.g. for ``GCSFileSystem`` it should look like `{"token": None}`.
        fs_args: Extra arguments to pass into underlying filesystem class constructor
            (e.g. `{"project": "my-project"}` for ``GCSFileSystem``), as well as
            to pass to the filesystem's `open` method through nested keys
            `open_args_load` and `open_args_save`.
            Here you can find all available arguments for `open`:
            https://filesystem-spec.readthedocs.io/en/latest/api.html#fsspec.spec.AbstractFileSystem.open
            All defaults are preserved, except `mode`, which is set to `r` when loading
            and to `w` when saving.
        metadata: Any arbitrary metadata.
            This is ignored by Kedro, but may be consumed by users or external plugins.

    Note: Here you can find all supported file formats: https://biopython.org/wiki/SeqIO
    """

    _fs_args = deepcopy(fs_args) or {}
    _fs_open_args_load = _fs_args.pop("open_args_load", {})
    _fs_open_args_save = _fs_args.pop("open_args_save", {})
    _credentials = deepcopy(credentials) or {}

    protocol, path = get_protocol_and_path(filepath)

    self._filepath = PurePosixPath(path)
    self._protocol = protocol
    if protocol == "file":
        _fs_args.setdefault("auto_mkdir", True)

    self._fs = fsspec.filesystem(self._protocol, **_credentials, **_fs_args)

    # Handle default load and save and fs arguments
    self._load_args = {**self.DEFAULT_LOAD_ARGS, **(load_args or {})}
    self._save_args = {**self.DEFAULT_SAVE_ARGS, **(save_args or {})}
    self._fs_open_args_load = {
        **self.DEFAULT_FS_ARGS.get("open_args_load", {}),
        **(_fs_open_args_load or {}),
    }
    self._fs_open_args_save = {
        **self.DEFAULT_FS_ARGS.get("open_args_save", {}),
        **(_fs_open_args_save or {}),
    }

    self.metadata = metadata

DEFAULT_FS_ARGS class-attribute instance-attribute

DEFAULT_FS_ARGS = {
    "open_args_save": {"mode": "w"},
    "open_args_load": {"mode": "r"},
}

DEFAULT_LOAD_ARGS class-attribute instance-attribute

DEFAULT_LOAD_ARGS = {}

DEFAULT_SAVE_ARGS class-attribute instance-attribute

DEFAULT_SAVE_ARGS = {}

_filepath instance-attribute

_filepath = PurePosixPath(path)

_fs instance-attribute

_fs = filesystem(_protocol, **_credentials, **_fs_args)

_fs_open_args_load instance-attribute

_fs_open_args_load = {
    None: get("open_args_load", {}),
    None: _fs_open_args_load or {},
}

_fs_open_args_save instance-attribute

_fs_open_args_save = {
    None: get("open_args_save", {}),
    None: _fs_open_args_save or {},
}

_load_args instance-attribute

_load_args = {
    None: DEFAULT_LOAD_ARGS,
    None: load_args or {},
}

_protocol instance-attribute

_protocol = protocol

_save_args instance-attribute

_save_args = {
    None: DEFAULT_SAVE_ARGS,
    None: save_args or {},
}

metadata instance-attribute

metadata = metadata

_describe

_describe()

Source code in kedro_datasets/biosequence/biosequence_dataset.py

def _describe(self) -> dict[str, Any]:
    return {
        "filepath": self._filepath,
        "protocol": self._protocol,
        "load_args": self._load_args,
        "save_args": self._save_args,
    }

_exists

_exists()

Source code in kedro_datasets/biosequence/biosequence_dataset.py

def _exists(self) -> bool:
    load_path = get_filepath_str(self._filepath, self._protocol)
    return self._fs.exists(load_path)

_release

_release()

Source code in kedro_datasets/biosequence/biosequence_dataset.py

def _release(self) -> None:
    self.invalidate_cache()

invalidate_cache

invalidate_cache()

Invalidate underlying filesystem caches.

Source code in kedro_datasets/biosequence/biosequence_dataset.py

def invalidate_cache(self) -> None:
    """Invalidate underlying filesystem caches."""
    filepath = get_filepath_str(self._filepath, self._protocol)
    self._fs.invalidate_cache(filepath)

load

load()

Source code in kedro_datasets/biosequence/biosequence_dataset.py

def load(self) -> list:
    load_path = get_filepath_str(self._filepath, self._protocol)
    with self._fs.open(load_path, **self._fs_open_args_load) as fs_file:
        return list(SeqIO.parse(handle=fs_file, **self._load_args))

save

save(data)

Source code in kedro_datasets/biosequence/biosequence_dataset.py

def save(self, data: list) -> None:
    save_path = get_filepath_str(self._filepath, self._protocol)

    with self._fs.open(save_path, **self._fs_open_args_save) as fs_file:
        SeqIO.write(data, handle=fs_file, **self._save_args)