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"""BioSequenceLocalDataSet loads and saves data to/from bio-sequence objects to
file.
"""
from os.path import isfile
from pathlib import Path
from typing import Any, Dict, List, Optional
from Bio import SeqIO
from kedro.contrib.io import DefaultArgumentsMixIn
from kedro.io import AbstractDataSet
from kedro.io.core import deprecation_warning
[docs]class BioSequenceLocalDataSet(DefaultArgumentsMixIn, AbstractDataSet):
"""``BioSequenceLocalDataSet`` loads and saves data to a sequence file.
Example:
::
>>> raw_sequence_list = [
>>> '>gi|2765658|emb|Z78533.1|CIZ78533'
>>> 'C.irapeanum 5.8S rRNA gene and ITS1 and ITS2 DNA'
>>> 'CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAA'
>>> 'CGATCGAGTGAATCCGGAGGACCGGTGTACTCAGCTCACCGGGGGCATTGCTCCCGTGGT'
>>> 'GACCCTGATTTGTTGTTGGGCCGCCTCGGGAGCGTCCATGGCGGGTTTGAACCTCTAGCC'
>>> 'CGGCGCAGTTTGGGCGCCAAGCCATATGAAAGCATCACCGGCGAATGGCATTGTCTTCCC'
>>> 'CAAAACCCGGAGCGGCGGCGTGCTGTCGCGTGCCCAATGAATTTTGATGACTCTCGCAAA'
>>> 'CGGGAATCTTGGCTCTTTGCATCGGATGGAAGGACGCAGCGAAATGCGATAAGTGGTGTG'
>>> 'AATTGCAAGATCCCGTGAACCATCGAGTCTTTTGAACGCAAGTTGCGCCCGAGGCCATCA'
>>> 'GGCTAAGGGCACGCCTGCTTGGGCGTCGCGCTTCGTCTCTCTCCTGCCAATGCTTGCCCG'
>>> 'GCATACAGCCAGGCCGGCGTGGTGCGGATGTGAAAGATTGGCCCCTTGTGCCTAGGTGCG'
>>> 'GCGGGTCCAAGAGCTGGTGTTTTGATGGCCCGGAACCCGGCAAGAGGTGGACGGATGCTG'
>>> 'GCAGCAGCTGCCGTGCGAATCCCCCATGTTGTCGTGCTTGTCGGACAGGCAGGAGAACCC'
>>> 'TTCCGAACCCCAATGGAGGGCGGTTGACCGCCATTCGGATGTGACCCCAGGTCAGGCGGG'
>>> 'GGCACCCGCTGAGTTTACGC']
>>> data_set = BioSequenceLocalDataSet(filepath="ls_orchid.fasta",
>>> load_args={"format": "fasta"},
>>> save_args={"format": "fasta"})
>>> data_set.save(raw_sequence_list)
>>> sequence_list = data_set.load()
>>> assert raw_sequence_list.equals(sequence_list)
"""
def _describe(self) -> Dict[str, Any]:
return dict(
filepath=self._filepath,
load_args=self._load_args,
save_args=self._save_args,
)
[docs] def __init__(
self,
filepath: str,
load_args: Optional[Dict[str, Any]] = None,
save_args: Optional[Dict[str, Any]] = None,
) -> None:
"""
Creates a new instance of ``BioSequenceLocalDataSet`` pointing
to a concrete filepath.
Args:
filepath: path to sequence file
load_args: Options for loading sequence files. Here you can find
all supported file formats: https://biopython.org/wiki/SeqIO
save_args: args supported by Biopython are 'handle' and 'format'.
Handle by default is equal to ``filepath``.
"""
deprecation_warning(self.__class__.__name__)
self._filepath = filepath
super().__init__(load_args, save_args)
def _load(self) -> List:
return list(SeqIO.parse(self._filepath, **self._load_args))
def _save(self, data: list) -> None:
save_path = Path(self._filepath)
save_path.parent.mkdir(parents=True, exist_ok=True)
SeqIO.write(data, handle=str(save_path), **self._save_args)
def _exists(self) -> bool:
return isfile(self._filepath)