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--- |
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license: apache-2.0 |
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--- |
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## Overview |
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This dataset consists of reference genomes for 10 species: |
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| Species | Assembly Accession | |
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|--------------------------|-----------------------------------------------------| |
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| *Arabidopsis thaliana* | `GCF_000001735.4_TAIR10.1` | |
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| *Caenorhabditis elegans* | `GCF_000002985.6_WBcel235` | |
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| *Danio rerio* | `GCF_000002035.6_GRCz11` | |
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| *Drosophila melanogaster*| `GCF_000001215.4_Release_6_plus_ISO1_MT` | |
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| *Felis catus* | `GCF_018350175.1_F.catus_Fca126_mat1.0` | |
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| *Gallus gallus* | `GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b` | |
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| *Gorilla gorilla* | `GCF_029281585.2_NHGRI_mGorGor1-v2.0_pri` | |
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| *Homo sapiens* | `GCF_000001405.40_GRCh38.p14` | |
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| *Mus musculus* | `GCF_000001635.27_GRCm39` | |
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| *Salmo trutta* | `GCF_901001165.1_fSalTru1.1` | |
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Each item in the dataset contains the following fields: |
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``` |
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"sequence": datasets.Value("string"), |
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"species_label": datasets.ClassLabel() # See below |
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"description": datasets.Value("string"), |
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"start_pos": datasets.Value("int32"), |
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"end_pos": datasets.Value("int32"), |
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"fasta_url": datasets.Value("string") |
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``` |
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The class labels are as follows: |
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| Class | Label | |
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|-----------------------------|-------| |
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| `'Homo_sapiens'` | 0 | |
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| `'Mus_musculus'` | 1 | |
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| `'Drosophila_melanogaster'` | 2 | |
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| `'Danio_rerio'` | 3 | |
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| `'Caenorhabditis_elegans'` | 4 | |
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| `'Gallus_gallus'` | 5 | |
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| `'Gorilla_gorilla'` | 6 | |
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| `'Felis_catus'` | 7 | |
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| `'Salmo_trutta'` | 8 | |
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| `'Arabidopsis_thaliana'` | 9 | |
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## Usage |
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To use this dataset, set the `chunk_length` (length of each sequence, in base-pairs) and the `overlap` (amount each sequence overlaps, in base-pairs). |
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The dataset only contains a `train` split. |
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We recommend randomly splitting the dataset to create validation/test sets. |
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See below for example usage: |
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```python |
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import datasets |
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max_length = 32_768 |
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overlap = 0 |
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dataset = datasets.load_dataset( |
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'yairschiff/ten_species', |
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split='train', # original dataset only has `train` split |
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chunk_length=max_length, |
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overlap=overlap, |
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trust_remote_code=True |
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) |
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self.dataset = dataset.train_test_split( |
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test_size=0.05, seed=42)[split] |
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``` |
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## Acknowledgments |
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Code for dataset processing is derived from https://huggingface.co/datasets/InstaDeepAI/multi_species_genomes. |
