pmillana commited on
Commit
86da93b
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1 Parent(s): 09d2f72

DEV: Add a load script

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This load script should separate the partitions according to the "split" column

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  1. dataset.py +53 -0
dataset.py ADDED
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+ import csv
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+ import datasets
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+
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+ class DNABarcodeDataset(datasets.GeneratorBasedBuilder):
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+ def _info(self):
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+ return datasets.DatasetInfo(
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+ description="DNA barcode dataset with hierarchical taxonomy labels and multiple splits.",
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+ features=datasets.Features({
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+ "processid": datasets.Value("string"),
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+ "sampleid": datasets.Value("string"),
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+ "dna_bin": datasets.Value("string"),
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+ "phylum": datasets.Value("string"),
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+ "class": datasets.Value("string"),
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+ "order": datasets.Value("string"),
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+ "family": datasets.Value("string"),
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+ "genus": datasets.Value("string"),
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+ "species": datasets.Value("string"), # label
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+ "dna_barcode": datasets.Value("string"), # input data
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+ "split": datasets.ClassLabel(names=["train", "val", "test", "test_unseen", "pretrain"]),
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+ }),
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+ supervised_keys=("dna_barcode", "species"), # For model training
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+ )
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+
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+ def _split_generators(self, dl_manager):
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+ data_path = dl_manager.download("CanInv_metadata.csv") # Use a URL or relative path
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+ return [
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+ datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_path, "split": "train"}),
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+ datasets.SplitGenerator(name=datasets.Split.VALIDATION, gen_kwargs={"filepath": data_path, "split": "val"}),
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+ datasets.SplitGenerator(name=datasets.Split.TEST, gen_kwargs={"filepath": data_path, "split": "test"}),
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+ datasets.SplitGenerator(name="test_unseen", gen_kwargs={"filepath": data_path, "split": "test_unseen"}),
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+ datasets.SplitGenerator(name="pretrain", gen_kwargs={"filepath": data_path, "split": "pretrain"}),
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+ ]
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+
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+ def _generate_examples(self, filepath, split):
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+ with open(filepath, encoding="utf-8") as f:
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+ reader = csv.DictReader(f)
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+ idx = 0
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+ for row in reader:
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+ if row["split"] == split:
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+ yield idx, {
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+ "processid": row["processid"],
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+ "sampleid": row["sampleid"],
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+ "dna_bin": row["dna_bin"],
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+ "phylum": row["phylum"],
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+ "class": row["class"],
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+ "order": row["order"],
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+ "family": row["family"],
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+ "genus": row["genus"],
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+ "species": row["species"],
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+ "dna_barcode": row["dna_barcode"],
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+ "split": row["split"],
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+ }
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+ idx += 1