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import csv
import datasets
class DNABarcodeDataset(datasets.GeneratorBasedBuilder):
def _info(self):
return datasets.DatasetInfo(
description="DNA barcode dataset with hierarchical taxonomy labels and multiple splits.",
features=datasets.Features({
"processid": datasets.Value("string"),
"sampleid": datasets.Value("string"),
"dna_bin": datasets.Value("string"),
"phylum": datasets.Value("string"),
"class": datasets.Value("string"),
"order": datasets.Value("string"),
"family": datasets.Value("string"),
"genus": datasets.Value("string"),
"species": datasets.Value("string"), # label
"dna_barcode": datasets.Value("string"), # input data
"split": datasets.ClassLabel(names=["train", "val", "test", "test_unseen", "pretrain"]),
}),
supervised_keys=("dna_barcode", "species"), # For model training
)
def _split_generators(self, dl_manager):
data_path = dl_manager.download("https://huggingface.co/datasets/bioscan-ml/CanadianInvertebrates-ML/resolve/main/CanInv_metadata.csv") # Use a URL or relative path
return [
datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_path, "split": "train"}),
datasets.SplitGenerator(name=datasets.Split.VALIDATION, gen_kwargs={"filepath": data_path, "split": "val"}),
datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": data_path, "split": "test"}),
datasets.SplitGenerator(name="test_unseen", gen_kwargs={"filepath": data_path, "split": "test_unseen"}),
datasets.SplitGenerator(name="pretrain", gen_kwargs={"filepath": data_path, "split": "pretrain"}),
]
def _generate_examples(self, filepath, split):
with open(filepath, encoding="utf-8") as f:
reader = csv.DictReader(f)
idx = 0
for row in reader:
if row["split"] == split:
yield idx, {
"processid": row["processid"],
"sampleid": row["sampleid"],
"dna_bin": row["dna_bin"],
"phylum": row["phylum"],
"class": row["class"],
"order": row["order"],
"family": row["family"],
"genus": row["genus"],
"species": row["species"],
"dna_barcode": row["dna_barcode"],
"split": row["split"],
}
idx += 1 |