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Datasets:
suke-sho
/
athaliana-genome-corpus

Tags:
biology
dna
License:
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The dataset viewer is not available for this dataset.
The dataset tries to import a module that is not installed.
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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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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