kedro.extras.datasets.biosequence.BioSequenceDataSet

class documentation

class BioSequenceDataSet(AbstractDataSet[List, List]): (source)

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

Method	`__init__`	Creates a new instance of `BioSequenceDataSet` pointing to a concrete filepath.
Method	`invalidate_cache`	Invalidate underlying filesystem caches.
Constant	`DEFAULT_LOAD_ARGS`	Undocumented
Constant	`DEFAULT_SAVE_ARGS`	Undocumented
Method	`_describe`	Undocumented
Method	`_exists`	Undocumented
Method	`_load`	Undocumented
Method	`_release`	Undocumented
Method	`_save`	Undocumented
Instance Variable	`_filepath`	Undocumented
Instance Variable	`_fs`	Undocumented
Instance Variable	`_fs_open_args_load`	Undocumented
Instance Variable	`_fs_open_args_save`	Undocumented
Instance Variable	`_load_args`	Undocumented
Instance Variable	`_protocol`	Undocumented
Instance Variable	`_save_args`	Undocumented

Inherited from AbstractDataSet:

Class Method	`from_config`	Create a data set instance using the configuration provided.
Method	`__str__`	Undocumented
Method	`exists`	Checks whether a data set's output already exists by calling the provided _exists() method.
Method	`load`	Loads data by delegation to the provided load method.
Method	`release`	Release any cached data.
Method	`save`	Saves data by delegation to the provided save method.
Method	`_copy`	Undocumented
Property	`_logger`	Undocumented

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): (source) ¶

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

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

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]`	Options for parsing sequence files by Biopython `SeqIO.parse()`.
save_args:`Dict[str, Any]`	file format supported by Biopython `SeqIO.write()`. E.g. `{"format": "fasta"}`.
credentials:`Dict[str, Any]`	Credentials required to get access to the underlying filesystem. E.g. for `GCSFileSystem` it should look like `{"token": None}`.
fs_args:`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.