First version of epigenetic_marks_pham2005 dataset

README.md

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+---
+dataset_info:
+- config_name: h3
+  features:
+  - name: description
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: label
+    dtype: int32
+  splits:
+  - name: fold0
+    num_bytes: 2641639
+    num_examples: 4988
+  - name: fold1
+    num_bytes: 2641787
+    num_examples: 4988
+  - name: fold2
+    num_bytes: 2642499
+    num_examples: 4989
+  download_size: 7806318
+  dataset_size: 7925925
+- config_name: h4
+  features:
+  - name: description
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: label
+    dtype: int32
+  splits:
+  - name: fold0
+    num_bytes: 2576509
+    num_examples: 4867
+  - name: fold1
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+    num_examples: 4867
+  - name: fold2
+    num_bytes: 2577112
+    num_examples: 4867
+  download_size: 7613876
+  dataset_size: 7730579
+- config_name: h3k9ac
+  features:
+  - name: description
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: label
+    dtype: int32
+  splits:
+  - name: fold0
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+    num_examples: 9260
+  - name: fold1
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+    num_examples: 9261
+  - name: fold2
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+    num_examples: 9261
+  download_size: 14504069
+  dataset_size: 14726184
+- config_name: h3k14ac
+  features:
+  - name: description
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: label
+    dtype: int32
+  splits:
+  - name: fold0
+    num_bytes: 5840246
+    num_examples: 11016
+  - name: fold1
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+    num_examples: 11016
+  - name: fold2
+    num_bytes: 5840196
+    num_examples: 11016
+  download_size: 17256808
+  dataset_size: 17520983
+- config_name: h3k4me1
+  features:
+  - name: description
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: label
+    dtype: int32
+  splits:
+  - name: fold0
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+    num_examples: 10559
+  - name: fold1
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+    num_examples: 10559
+  - name: fold2
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+    num_examples: 10559
+  download_size: 16543265
+  dataset_size: 16796500
+- config_name: h3k4me2
+  features:
+  - name: description
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: label
+    dtype: int32
+  splits:
+  - name: fold0
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+    num_examples: 10227
+  - name: fold1
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+    num_examples: 10228
+  - name: fold2
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+    num_examples: 10228
+  download_size: 16026783
+  dataset_size: 16272042
+- config_name: h3k36me3
+  features:
+  - name: description
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: label
+    dtype: int32
+  splits:
+  - name: fold0
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+    num_examples: 11626
+  - name: fold1
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+    num_examples: 11627
+  - name: fold2
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+    num_examples: 11627
+  download_size: 18215056
+  dataset_size: 18493899
+- config_name: h3k79me3
+  features:
+  - name: description
+    dtype: string
+  - name: sequence
+    dtype: string
+  - name: label
+    dtype: int32
+  splits:
+  - name: fold0
+    num_bytes: 5095638
+    num_examples: 9612
+  - name: fold1
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+    num_examples: 9612
+  - name: fold2
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+    num_examples: 9613
+  download_size: 15056451
+  dataset_size: 15286998
+---

epigenetic_marks_pham2005.py

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+# 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.
+# TODO: Address all TODOs and remove all explanatory comments
+"""TODO: Add a description here."""
+
+
+import csv
+import json
+import os
+
+import datasets
+
+
+_CITATION = """\
+    @article{pham2005qualitatively,
+  title={Qualitatively predicting acetylation and methylation areas in dna sequences},
+  author={Pham, Tho Hoan and Tran, Dang Hung and Ho, Tu Bao and Satou, Kenji and Valiente, Gabriel},
+  journal={Genome Informatics},
+  volume={16},
+  number={2},
+  pages={3--11},
+  year={2005},
+  publisher={Japanese Society for Bioinformatics}
+}
+"""
+
+_LICENSE = ""
+
+_DESCRIPTION = """\
+    This contains datasets of histone occupancy, acetylation, and methylation by ChiP-Chip protocol in vivo from Pham et al., as retrieved from https://www.jaist.ac.jp/~tran/nucleosome/members.htm in January 2023.
+"""
+
+_HOMEPAGE = "https://www.jaist.ac.jp/~tran/nucleosome/"
+
+FILES = {
+    "h3": [
+        "data/processed/h3/fold_0.csv",
+        "data/processed/h3/fold_1.csv",
+        "data/processed/h3/fold_2.csv",
+    ],
+    "h3k14ac": [
+        "data/processed/h3k14ac/fold_0.csv",
+        "data/processed/h3k14ac/fold_1.csv",
+        "data/processed/h3k14ac/fold_2.csv",
+    ],
+    "h3k36me3": [
+        "data/processed/h3k36me3/fold_0.csv",
+        "data/processed/h3k36me3/fold_1.csv",
+        "data/processed/h3k36me3/fold_2.csv",
+    ],
+    "h3k4me1": [
+        "data/processed/h3k4me1/fold_0.csv",
+        "data/processed/h3k4me1/fold_1.csv",
+        "data/processed/h3k4me1/fold_2.csv",
+    ],
+    "h3k4me2": [
+        "data/processed/h3k4me2/fold_0.csv",
+        "data/processed/h3k4me2/fold_1.csv",
+        "data/processed/h3k4me2/fold_2.csv",
+    ],
+    "h3k79me3": [
+        "data/processed/h3k79me3/fold_0.csv",
+        "data/processed/h3k79me3/fold_1.csv",
+        "data/processed/h3k79me3/fold_2.csv",
+    ],
+    "h3k9ac": [
+        "data/processed/h3k9ac/fold_0.csv",
+        "data/processed/h3k9ac/fold_1.csv",
+        "data/processed/h3k9ac/fold_2.csv",
+    ],
+    "h4": [
+        "data/processed/h4/fold_0.csv",
+        "data/processed/h4/fold_1.csv",
+        "data/processed/h4/fold_2.csv",
+    ],
+}
+
+
+class EpigeneticMarks(datasets.GeneratorBasedBuilder):
+    """
+    This contains datasets of histone occupancy, acetylation, and methylation by ChiP-Chip protocol in vivo from Pham et al., as retrieved from https://www.jaist.ac.jp/~tran/nucleosome/members.htm in January 2023.
+    """
+
+    VERSION = datasets.Version("0.0.1")
+
+    # data = datasets.load_dataset('my_dataset', 'first_domain')
+    # data = datasets.load_dataset('my_dataset', 'second_domain')
+
+    BUILDER_CONFIGS = [
+        datasets.BuilderConfig(
+            name="h3",
+            version=VERSION,
+            description="H3 occupancy",
+        ),
+        datasets.BuilderConfig(
+            name="h4",
+            version=VERSION,
+            description="H4 occupancy",
+        ),
+        datasets.BuilderConfig(
+            name="h3k9ac",
+            version=VERSION,
+            description="H3K9 acetylation relative to H3",
+        ),
+        datasets.BuilderConfig(
+            name="h3k14ac",
+            version=VERSION,
+            description="H3K14 acetylation relative to H3",
+        ),
+        # datasets.BuilderConfig(
+        #     name="h4ac",
+        #     version=VERSION,
+        #     description="H4 acetylation relative to H3",
+        # ),
+        datasets.BuilderConfig(
+            name="h3k4me1",
+            version=VERSION,
+            description="H3K4 monomethylation relative to H3",
+        ),
+        datasets.BuilderConfig(
+            name="h3k4me2",
+            version=VERSION,
+            description="H3K4 dimethylation relative to H3",
+        ),
+        # datasets.BuilderConfig(
+        #     name="h3k4me3",
+        #     version=VERSION,
+        #     description="H3K4 trimethylation relative to H3",
+        # ),
+        datasets.BuilderConfig(
+            name="h3k36me3",
+            version=VERSION,
+            description="H3K36 trimethylation relative to H3",
+        ),
+        datasets.BuilderConfig(
+            name="h3k79me3",
+            version=VERSION,
+            description="H3K79 trimethylation relative to H3",
+        ),
+    ]
+    DEFAULT_CONFIG_NAME = "h3"
+
+    def _info(self):
+        features = datasets.Features(
+            {
+                "description": datasets.Value("string"),
+                "sequence": datasets.Value("string"),
+                "label": datasets.Value("int32"),
+            }
+        )
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            supervised_keys=("sequence", "label"),
+            homepage=_HOMEPAGE,
+            license=_LICENSE,
+            citation=_CITATION,
+        )
+
+    def _split_generators(self, dl_manager):
+        dataset = self.config.name
+
+        downloaded_files = dl_manager.download(FILES[dataset])
+
+        return [
+            datasets.SplitGenerator(
+                name=datasets.NamedSplit("fold0"),
+                # These kwargs will be passed to _generate_examples
+                gen_kwargs={
+                    "filepath": downloaded_files[0],
+                },
+            ),
+            datasets.SplitGenerator(
+                name=datasets.NamedSplit("fold1"),
+                # These kwargs will be passed to _generate_examples
+                gen_kwargs={
+                    "filepath": downloaded_files[1],
+                },
+            ),
+            datasets.SplitGenerator(
+                name=datasets.NamedSplit("fold2"),
+                # These kwargs will be passed to _generate_examples
+                gen_kwargs={
+                    "filepath": downloaded_files[2],
+                },
+            ),
+        ]
+
+    # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
+    def _generate_examples(self, filepath):
+        with open(filepath) as f:
+            reader = csv.DictReader(f)
+            for key, data in enumerate(reader):
+                yield key, {
+                    "description": data["description"],
+                    "sequence": data["sequence"],
+                    "label": data["label"],
+                }