| import os |
| import datasets |
|
|
|
|
| logger = datasets.logging.get_logger(__name__) |
|
|
| ID_POOL = () |
| URL = "https://huggingface.co/datasets/thewall/DeepBindWeight/resolve/main" |
|
|
|
|
| class DeepBindWeightConfig(datasets.BuilderConfig): |
| pass |
|
|
|
|
| class DeepBindWeight(datasets.GeneratorBasedBuilder): |
| BUILDER_CONFIGS = [ |
| DeepBindWeightConfig(name=key) for key in ID_POOL |
| ] |
|
|
| DEFAULT_CONFIG_NAME = "params" |
|
|
| def _info(self): |
| return datasets.DatasetInfo( |
| features=datasets.Features( |
| { |
| "config": datasets.Value("string"), |
| "existed": datasets.Value("bool"), |
| "selex": datasets.Value("string"), |
| "tf": datasets.Value("string") |
| } |
| ), |
| homepage="http://tools.genes.toronto.edu/deepbind", |
| ) |
|
|
| def _split_generators(self, dl_manager): |
| param_url = f"{URL}/params.tar.gz" |
| selex_url = f"{URL}/ERP001824-deepbind.xlsx" |
| tf_url = f"{URL}/ERP001824-UniprotKB.xlsx" |
| aptani2_url = f"{URL}/aptani2_config.tar.gz" |
| downloaded_files = [os.path.join(f"{dl_manager.download_and_extract(param_url)}", "params")] |
| downloaded_files.extend(dl_manager.download([selex_url, tf_url])) |
| downloaded_files.append(f"{dl_manager.download_and_extract(aptani2_url)}") |
| return [ |
| datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloaded_files}), |
| ] |
|
|
| def _generate_examples(self, filepath): |
| """This function returns the examples in the raw (text) form.""" |
| logger.info("generating examples from = %s", filepath) |
| flag = True |
| for file in filepath: |
| flag = flag and os.path.exists(file) |
| |
| yield 0, {"config": filepath[0], |
| "existed": flag, |
| "selex": filepath[1], |
| 'tf': filepath[2]} |
|
|
|
|
| if __name__=="__main__": |
| from datasets import load_dataset |
| dataset = load_dataset("thewall/deepbindweight", split="all") |
| |
|
|
