Source code for kedro.extras.datasets.biosequence.biosequence_dataset

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"""BioSequenceDataSet loads and saves data to/from bio-sequence objects to
file.
"""
from copy import deepcopy
from pathlib import PurePosixPath
from typing import Any, Dict, List

import fsspec
from Bio import SeqIO

from kedro.io.core import AbstractDataSet, get_filepath_str, get_protocol_and_path


[docs]class BioSequenceDataSet(AbstractDataSet): r"""``BioSequenceDataSet`` loads and saves data to a sequence file. Example: :: >>> from kedro.extras.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) >>> >>> data_set = BioSequenceDataSet(filepath="ls_orchid.fasta", >>> load_args={"format": "fasta"}, >>> save_args={"format": "fasta"}) >>> data_set.save(raw_data) >>> sequence_list = data_set.load() >>> >>> assert raw_data[0].id == sequence_list[0].id >>> assert raw_data[0].seq == sequence_list[0].seq """ DEFAULT_LOAD_ARGS = {} # type: Dict[str, Any] DEFAULT_SAVE_ARGS = {} # type: Dict[str, Any] # pylint: disable=too-many-arguments
[docs] def __init__( 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, ) -> 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. 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 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
def _describe(self) -> Dict[str, Any]: return dict( 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)