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Cannot get the config names for the dataset.
Error code: ConfigNamesError
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 66, 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 1914, in dataset_module_factory
raise e1 from None
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1880, in dataset_module_factory
return HubDatasetModuleFactoryWithScript(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1504, in get_module
local_imports = _download_additional_modules(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 354, 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.Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
Dataset Card for Arabidopsis Genome Corpus
Dataset Description
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.
Dataset Summary
- Homepage: NCBI
- License: NCBI Policies
- Version: 1.1.0
- Size: Variable depending on the configuration
- Default Configuration: 6kbp chunks
Usage Example
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)
Acknowledgments
This dataset is an adaptation of the "InstaDeepAI/plant-multi-species-genomes" dataset & script. Special thanks to InstaDeepAI for their original work.
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