"""BioSequenceDataset loads and saves data to/from bio-sequence objects to
file.
"""
from copy import deepcopy
from pathlib import PurePosixPath
from typing import Any
import fsspec
from Bio import SeqIO
from kedro.io.core import AbstractDataset, get_filepath_str, get_protocol_and_path
[docs]
class BioSequenceDataset(AbstractDataset[list, list]):
r"""``BioSequenceDataset`` loads and saves data to a sequence file.
Example:
.. code-block:: pycon
>>> 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
"""
DEFAULT_LOAD_ARGS: dict[str, Any] = {}
DEFAULT_SAVE_ARGS: dict[str, Any] = {}
[docs]
def __init__( # noqa: PLR0913
self,
*,
filepath: str,
load_args: dict[str, Any] = None,
save_args: dict[str, Any] = None,
credentials: dict[str, Any] = None,
fs_args: dict[str, Any] = None,
metadata: dict[str, Any] = 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 arguments
self._load_args = deepcopy(self.DEFAULT_LOAD_ARGS)
if load_args is not None:
self._load_args.update(load_args)
self._save_args = deepcopy(self.DEFAULT_SAVE_ARGS)
if save_args is not None:
self._save_args.update(save_args)
_fs_open_args_load.setdefault("mode", "r")
_fs_open_args_save.setdefault("mode", "w")
self._fs_open_args_load = _fs_open_args_load
self._fs_open_args_save = _fs_open_args_save
self.metadata = metadata
def _describe(self) -> dict[str, Any]:
return {
"filepath": self._filepath,
"protocol": self._protocol,
"load_args": self._load_args,
"save_args": self._save_args,
}
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))
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)
def _exists(self) -> bool:
load_path = get_filepath_str(self._filepath, self._protocol)
return self._fs.exists(load_path)
def _release(self) -> None:
self.invalidate_cache()
[docs]
def invalidate_cache(self) -> None:
"""Invalidate underlying filesystem caches."""
filepath = get_filepath_str(self._filepath, self._protocol)
self._fs.invalidate_cache(filepath)
