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hg38.py
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# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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import json
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import os
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import datasets
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import pandas as pd
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_CITATION = """\
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CITATION
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"""
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_DESCRIPTION = """\
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DESCRIPTION
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"""
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_HOMEPAGE = "HOMEPAGE"
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_LICENSE = ""
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FILES = ["hg38_8k_train.jsonl", "hg38_8k_test.jsonl"]
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task_list = [
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"hg38_8k",
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]
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class hg38Config(datasets.BuilderConfig):
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def __init__(self, **kwargs):
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super().__init__(version=datasets.Version("1.0.0"), **kwargs)
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class hg38(datasets.GeneratorBasedBuilder):
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BUILDER_CONFIGS = [
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hg38Config(
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name=task_name,
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)
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for task_name in task_list
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]
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def _info(self):
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return datasets.DatasetInfo(
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description=_DESCRIPTION,
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features=datasets.Features(
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{
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"chrom":datasets.Value("string"),
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"start": datasets.Value("int32"),
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"end": datasets.Value("int32"),
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"seq": datasets.Value("string"),
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}
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),
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homepage=_HOMEPAGE,
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license=_LICENSE,
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citation=_CITATION,
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)
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def _split_generators(self, dl_manager):
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downloaded_files = dl_manager.download(FILES)
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return [
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datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files[0]}),
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datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": downloaded_files[1]}),
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]
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def _generate_examples(self, filepath):
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with open(filepath) as jsonl_file:
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for row, line in enumerate(jsonl_file):
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data = json.loads(line)
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yield row, {
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"chrom": data["chrom"],
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"start": data["start"],
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"end": data["end"],
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"seq": data["seq"],
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}
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