rnaglib.data_loading

Tools for loading and creating collections of RNAs.

RNA Dataset

This is the main object used for holding collections of RNAs. The RNAdataset object draws from a database.

RNADataset([rnas, dataset_path, ...])

This class is the main object to hold the core RNA data annotations.

Loading

Tools for loading RNAs stored in an RNADataset batch-wise for deep learning models.

Collater(dataset)

Wrapper for collate function, so we can use different node similarities.

get_loader(dataset[, batch_size, ...])

Fetch a loader object for a given dataset.

get_inference_loader(list_to_predict[, ...])

This is to just make an inference over a list of graphs.

EdgeLoaderGenerator(graph_loader[, ...])

This turns a graph dataloader or dataset into an edge data loader generator.

DefaultBasePairLoader([dataset, data_path, ...])

Dataloader that yields base pairs