crested.tl.data.AnnDataWrapper

crested.tl.data.AnnDataWrapper#

class crested.tl.data.AnnDataWrapper(data, genome=None, batch_size=256, random_reverse_complement=False, always_reverse_complement=True, max_stochastic_shift=0, in_memory=True, drop_remainder=False, train_splits=None, val_splits='val', test_splits='test', split_column='split', **kwargs)#

Wrapper around your AnnData and genome, providing you with one-hot encoded sequences and associated scalar values to train a model with.

The Crested class expects this or AnnDataModule.

Parameters:

  • data (AnnData) – Your AnnData object.

  • genome (Genome | None (default: None)) – The genome to extract sequences from, as a crested.Genome object. If None, will look up the registered Genome.

  • batch_size (int (default: 256)) – Batch size to use during training and evaluation.

  • random_reverse_complement (bool (default: False)) – If True, the sequences will be randomly reverse complemented during training. Incompatible with always_reverse_complement.

  • always_reverse_complement (bool (default: True)) – If True, the dataset will be expanded to include both the forward and reverse-complemented versions of every entry in the training set. Incompatible with random_reverse_complement.

  • max_stochastic_shift (int (default: 0)) – Maximum stochastic shift (n base pairs in either direction) to apply randomly to each sequence during training. Default is 0 (disabled).

  • drop_remainder (bool (default: False)) – If True, drop the last batch if it is not the full batch_size. Default is False.

  • train_splits (str | list | None (default: None)) – The values in your split labeling that correspond to the training set as string or list of strings, i.e ‘train’ or [‘fold0’, ‘fold1’, ‘fold2’] If None, uses the values that aren’t val_splits or test_splits.

  • val_splits (str | list (default: 'val')) – The values in your split labeling that correspond to the validation set as string or list of strings, i.e ‘val’ or [‘fold3’, ‘fold4’]

  • test_splits (str | list (default: 'test')) – The values in your split labeling that correspond to the test set as string or list of strings, i.e ‘test’ or [‘fold5’, ‘fold6’]

  • split_column (str (default: 'split')) – The column in adata.var that contains the values to split on (as provided to [train/val/test]_splits)

  • kwargs – Arguments passed to BaseGenomicDataWrapper.

Attributes table#

Methods table#

get_config()

Return a dict of properties, to be logged during training.

Attributes#

Methods#

AnnDataWrapper.get_config()#

Return a dict of properties, to be logged during training.

Primarily used in Crested.fit().

Return type:

dict