Create genome_origin_datasets.py

genome_origin_datasets.py

@@ -0,0 +1,112 @@
+# 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 tasks for genome origin detection."""
+
+from typing import List
+
+import datasets
+
+
+# Custom function to parse lines in the dataset
+def parse_text(fp):
+    for line in fp:
+        line = line.strip()
+        if not line:  # Skip empty lines
+            continue
+        seq, label = line.split(",")
+        yield seq, label
+
+
+# Dataset metadata
+_CITATION = """TBD"""
+_DESCRIPTION = """TBD"""
+_HOMEPAGE = "TBD"
+_LICENSE = "TBD"
+
+# Tasks available in the dataset
+_TASKS = [
+    "four_kingdoms",
+    "plasmid_detection",
+]
+
+
+class GenomeOriginTasksConfig(datasets.BuilderConfig):
+    """BuilderConfig for Genome Origin tasks dataset."""
+
+    def __init__(self, *args, task: str, **kwargs):
+        """
+        BuilderConfig for Genome Origin tasks dataset.
+
+        Args:
+            task (str): Task name.
+            **kwargs: Additional keyword arguments forwarded to super.
+        """
+        super().__init__(
+            *args,
+            name=f"{task}",
+            **kwargs,
+        )
+        self.task = task
+
+
+class GenomeOriginTasks(datasets.GeneratorBasedBuilder):
+    VERSION = datasets.Version("1.1.0")
+    BUILDER_CONFIG_CLASS = GenomeOriginTasksConfig
+    BUILDER_CONFIGS = [GenomeOriginTasksConfig(task=task) for task in _TASKS]
+    DEFAULT_CONFIG_NAME = "four_kingdoms"
+
+    def _info(self):
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=datasets.Features(
+                {
+                    "sequence": datasets.Value("string"),
+                    "label": datasets.Value("int32"),
+                }
+            ),
+            homepage=_HOMEPAGE,
+            license=_LICENSE,
+            citation=_CITATION,
+        )
+
+    def _split_generators(self, dl_manager: datasets.DownloadManager) -> List[datasets.SplitGenerator]:
+        """Returns SplitGenerators."""
+
+        task_dir = dl_manager.download_and_extract(self.config.task)
+        # base_url = "https://huggingface.co/datasets/mahdibaghbanzadeh/genome_origin_datasets/resolve/main"
+        # task_dir = f"{base_url}/{self.config.task}"
+
+        train_file = f"{task_dir}/train.txt"
+        test_file = f"{task_dir}/test.txt"
+
+        return [
+            datasets.SplitGenerator(
+                name=datasets.Split.TRAIN, gen_kwargs={"file_path": train_file}
+            ),
+            datasets.SplitGenerator(
+                name=datasets.Split.TEST, gen_kwargs={"file_path": test_file}
+            ),
+        ]
+
+    def _generate_examples(self, file_path):
+        """Generates examples from a given file."""
+        key = 0
+        with open(file_path, "r") as f:
+            for seq, label in parse_text(f):
+                yield key, {
+                    "sequence": seq.upper(),  # Ensure sequences are uppercase
+                    "label": int(label),  # Convert label to integer
+                }
+                key += 1