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Datasets:
twrightsman
/
phytozome_genomes

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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 twrightsman/phytozome_genomes, you need to install the following dependency: Bio.
Please install it using 'pip install Bio' for instance.
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 55, in compute_config_names_response
                  for config in sorted(get_dataset_config_names(path=dataset, token=hf_token))
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 351, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1512, in dataset_module_factory
                  raise e1 from None
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1481, in dataset_module_factory
                  return HubDatasetModuleFactoryWithScript(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1202, in get_module
                  local_imports = _download_additional_modules(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 294, in _download_additional_modules
                  raise ImportError(
              ImportError: To be able to use twrightsman/phytozome_genomes, you need to install the following dependency: Bio.
              Please install it using 'pip install Bio' for instance.

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Phytozome Genomes

This dataset consists of 100 current (as of 2023-06-20) unrestricted Phytozome genome assemblies, listed in genomes.tsv.

Currently, the training, validation, and test splits are a random 90/5/5% split, but this will change before version 1.0.

Individual observations are entire chromosomes/contigs, so it is up to the user to chunk them up further to their appropriate size.

Quickstart 

$ conda env create --file environment.yml
$ conda activate phytozome_genomes_dataset

import datasets
dataset = datasets.load_dataset('twrightsman/phytozome_genomes', username = 'my_jgi_username', password = 'my_jgi_password')
for observation in dataset['train']:
    # do cool stuff here, for example:
    seqid = observation['seqid']
    sequence = observation['sequence']
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