nucleotide_transformer_downstream_tasks.py

# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script
# contributor.
#
# 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
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Script for the dataset containing the 18 downstream tasks from the Nucleotide
Transformer paper."""

from typing import List

import datasets
from datasets.utils import logging

datasets.logging.set_verbosity(datasets.logging.WARNING)
logger = logging.get_logger("datasets")



# This function is a basic reimplementation of SeqIO's parse method. This allows the
# dataset viewer to work as it does not require an external package.
def parse_fasta(fp):
    name, seq = None, []
    for line in fp:
        line = line.rstrip()
        if line.startswith(">"):
            if name:
                # Slice to remove '>'
                yield (name[1:], "".join(seq))
            name, seq = line, []
        else:
            seq.append(line)
    if name:
        # Slice to remove '>'
        yield (name[1:], "".join(seq))


# Find for instance the citation on arxiv or on the dataset repo/website
_CITATION = """\
@article{dalla2023nucleotide,
  title={The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics},
  author={Dalla-Torre, Hugo and Gonzalez, Liam and Mendoza-Revilla, Javier and Carranza, Nicolas Lopez and Grzywaczewski, Adam Henryk and Oteri, Francesco and Dallago, Christian and Trop, Evan and Sirelkhatim, Hassan and Richard, Guillaume and others},
  journal={bioRxiv},
  pages={2023--01},
  year={2023},
  publisher={Cold Spring Harbor Laboratory}
}
"""

# You can copy an official description
_DESCRIPTION = """\
The 18 classification downstream tasks from the Nucleotide Transformer paper. Each task
corresponds to a dataset configuration.
"""

_HOMEPAGE = "https://github.com/instadeepai/nucleotide-transformer"

_LICENSE = "https://github.com/instadeepai/nucleotide-transformer/LICENSE.md"

_TASKS = [
    "H4ac",
    "H3K36me3",
    "splice_sites_donors",
    "splice_sites_acceptors",
    "H3",
    "H4",
    "H3K4me3",
    "splice_sites_all",
    "H3K4me1",
    "H3K14ac",
    "enhancers_types",
    "promoter_no_tata",
    "H3K79me3",
    "H3K4me2",
    "promoter_tata",
    "enhancers",
    "H3K9ac",
    "promoter_all",
]


class NucleotideTransformerDownstreamTasksConfig(datasets.BuilderConfig):
    """BuilderConfig for The Nucleotide Transformer downstream taks dataset."""

    def __init__(self, *args, task: str, **kwargs):
        """BuilderConfig downstream tasks dataset.
        Args:
            task (:obj:`str`): Task name.
            **kwargs: keyword arguments forwarded to super.
        """
        super().__init__(
            *args,
            name=f"{task}",
            **kwargs,
        )
        self.task = task
        


class NucleotideTransformerDownstreamTasks(datasets.GeneratorBasedBuilder):
    VERSION = datasets.Version("1.1.0")
    BUILDER_CONFIG_CLASS = NucleotideTransformerDownstreamTasksConfig
    BUILDER_CONFIGS = [
        NucleotideTransformerDownstreamTasksConfig(task=task) for task in _TASKS
    ]
    DEFAULT_CONFIG_NAME = "enhancers"

    def _info(self):

        features = datasets.Features(
            {
                "sequence": datasets.Value("string"),
                "name": datasets.Value("string"),
                "label": datasets.Value("int32"),
            }
        )
        return datasets.DatasetInfo(
            # This is the description that will appear on the datasets page.
            description=_DESCRIPTION,
            # This defines the different columns of the dataset and their types
            features=features,
            # Homepage of the dataset for documentation
            homepage=_HOMEPAGE,
            # License for the dataset if available
            license=_LICENSE,
            # Citation for the dataset
            citation=_CITATION,
        )

    def _split_generators(
        self, dl_manager: datasets.DownloadManager
    ) -> List[datasets.SplitGenerator]:

        
        train_file = dl_manager.download_and_extract(self.config.task + "/train.fna")
        test_file = dl_manager.download_and_extract(self.config.task + "/test.fna")

        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN, gen_kwargs={"file": train_file}
            ),
            datasets.SplitGenerator(
                name=datasets.Split.TEST, gen_kwargs={"file": test_file}
            ),
        ]

    # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
    def _generate_examples(self, file):
        
        logger.warning(""" 
                       
        WARNING: Please note that the Nucleotide Transformer benchmark datasets have been revised
        during the per-review process. This version is deprecated and the new datasets are available at 
        InstaDeepAI/nucleotide_transformer_downstream_tasks_revised.
                       
              """)
        key = 0
        with open(file, "rt") as f:
            fasta_sequences = parse_fasta(f)

            for name, seq in fasta_sequences:

                # parse descriptions in the fasta file
                sequence, name = str(seq), str(name)
                label = int(name.split("|")[-1])

                # yield example
                yield key, {
                    "sequence": sequence,
                    "name": name,
                    "label": label,
                }
                key += 1