Source code for kedro.contrib.io.bioinformatics.sequence_dataset

# Copyright 2018-2019 QuantumBlack Visual Analytics Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND
# NONINFRINGEMENT. IN NO EVENT WILL THE LICENSOR OR OTHER CONTRIBUTORS
# BE LIABLE FOR ANY CLAIM, DAMAGES, OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF, OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# The QuantumBlack Visual Analytics Limited (“QuantumBlack”) name and logo
# (either separately or in combination, “QuantumBlack Trademarks”) are
# trademarks of QuantumBlack. The License does not grant you any right or
# license to the QuantumBlack Trademarks. You may not use the QuantumBlack
# Trademarks or any confusingly similar mark as a trademark for your product,
#     or use the QuantumBlack Trademarks in any other manner that might cause
# confusion in the marketplace, including but not limited to in advertising,
# on websites, or on software.
#
# See the License for the specific language governing permissions and
# limitations under the License.

"""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.io import AbstractDataSet, ExistsMixin


[docs]class BioSequenceLocalDataSet(AbstractDataSet, ExistsMixin): """``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``. """ self._filepath = filepath default_load_args = {} default_save_args = {} self._load_args = ( {**default_load_args, **load_args} if load_args is not None else default_load_args ) self._save_args = ( {**default_save_args, **save_args} if save_args is not None else default_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)