kedro_datasets.biosequence.BioSequenceDataset

class kedro_datasets.biosequence.BioSequenceDataset(*, filepath, load_args=None, save_args=None, credentials=None, fs_args=None, metadata=None)

BioSequenceDataset loads and saves data to a sequence file.

Example:

 from kedro_datasets.biosequence import BioSequenceDataset
 from io import StringIO
 from Bio import SeqIO

 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

Attributes

DEFAULT_FS_ARGS
DEFAULT_LOAD_ARGS
DEFAULT_SAVE_ARGS

Methods

exists()	Checks whether a dataset's output already exists by calling the provided _exists() method.
from_config(name, config[, load_version, ...])	Create a dataset instance using the configuration provided.
invalidate_cache()	Invalidate underlying filesystem caches.
load()	Loads data by delegation to the provided load method.
release()	Release any cached data.
save(data)	Saves data by delegation to the provided save method.
to_config()	Converts the dataset instance into a dictionary-based configuration for serialization.

DEFAULT_FS_ARGS: dict[str, Any] = {'open_args_load': {'mode': 'r'}, 'open_args_save': {'mode': 'w'}}

DEFAULT_LOAD_ARGS: dict[str, Any] = {}

DEFAULT_SAVE_ARGS: dict[str, Any] = {}

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

Creates a new instance of BioSequenceDataset pointing to a concrete filepath.

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 (Optional[dict[str, Any]]) – Options for parsing sequence files by Biopython SeqIO.parse().

• save_args (Optional[dict[str, Any]]) – file format supported by Biopython SeqIO.write(). E.g. {“format”: “fasta”}.

• credentials (Optional[dict[str, Any]]) – Credentials required to get access to the underlying filesystem. E.g. for GCSFileSystem it should look like {“token”: None}.

• fs_args (Optional[dict[str, Any]]) – 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 (Optional[dict[str, Any]]) – 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

exists()

Checks whether a dataset’s output already exists by calling the provided _exists() method.

Return type:

bool

Returns:

Flag indicating whether the output already exists.

Raises:

DatasetError – when underlying exists method raises error.

classmethod from_config(name, config, load_version=None, save_version=None)

Create a dataset instance using the configuration provided.

Parameters:

• name (str) – Data set name.

• config (dict[str, Any]) – Data set config dictionary.

• load_version (Optional[str]) – Version string to be used for load operation if the dataset is versioned. Has no effect on the dataset if versioning was not enabled.

• save_version (Optional[str]) – Version string to be used for save operation if the dataset is versioned. Has no effect on the dataset if versioning was not enabled.

Return type:

AbstractDataset

Returns:

An instance of an AbstractDataset subclass.

Raises:

DatasetError – When the function fails to create the dataset from its config.

invalidate_cache()

Invalidate underlying filesystem caches.

Return type:

None

load()

Loads data by delegation to the provided load method.

Return type:

list

Returns:

Data returned by the provided load method.

Raises:

DatasetError – When underlying load method raises error.

release()

Release any cached data.

Raises:

DatasetError – when underlying release method raises error.

Return type:

None

save(data)

Saves data by delegation to the provided save method.

Parameters:

data (list) – the value to be saved by provided save method.

Raises:

• DatasetError – when underlying save method raises error.

• FileNotFoundError – when save method got file instead of dir, on Windows.

• NotADirectoryError – when save method got file instead of dir, on Unix.

Return type:

None

to_config()

Converts the dataset instance into a dictionary-based configuration for serialization. Ensures that any subclass-specific details are handled, with additional logic for versioning and caching implemented for CachedDataset.

Adds a key for the dataset’s type using its module and class name and includes the initialization arguments.

For CachedDataset it extracts the underlying dataset’s configuration, handles the versioned flag and removes unnecessary metadata. It also ensures the embedded dataset’s configuration is appropriately flattened or transformed.

If the dataset has a version key, it sets the versioned flag in the configuration.

Removes the metadata key from the configuration if present.

Return type:

dict[str, Any]

Returns:

A dictionary containing the dataset’s type and initialization arguments.