Kmer Plant BERT
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Error code: DatasetModuleNotInstalledError Exception: ImportError Message: To be able to use suke-sho/athaliana-genome-corpus, you need to install the following dependency: Bio. Please install it using 'pip install biopython' for instance. Traceback: Traceback (most recent call last): File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 73, in compute_config_names_response config_names = get_dataset_config_names( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 347, in get_dataset_config_names dataset_module = dataset_module_factory( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1910, in dataset_module_factory raise e1 from None File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1876, in dataset_module_factory return HubDatasetModuleFactoryWithScript( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1498, in get_module local_imports = _download_additional_modules( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 353, in _download_additional_modules raise ImportError( ImportError: To be able to use suke-sho/athaliana-genome-corpus, you need to install the following dependency: Bio. Please install it using 'pip install biopython' for instance.
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This dataset consists of model plant genomes available on NCBI, specifically processed and cleaned for research and pre-training purposes. The default configuration, "6kbp," provides DNA chunks of 6.2kbp with a 100bp overlap on each side. The sequences are cleaned and processed to contain only the letters A, T, C, G, and N, ensuring high-quality genomic data suitable for various bioinformatics and machine learning applications.
from datasets import load_dataset
# default chunk-size is 6000
chunk_length = 1024
repo = "suke-sho/arabidopsis_genome_corpus"
datasets = load_dataset(repo, trust_remote_code=True, chunk_length=chunk_length)
This dataset is an adaptation of the "InstaDeepAI/plant-multi-species-genomes" dataset & script. Special thanks to InstaDeepAI for their original work.