Utils

CREsted provides a few utility function to help with sequence encoding, function optimization, …

EnhancerOptimizer(optimize_func)	Class to optimize the mutated sequence based on the original prediction.
read_bigwig_region(bigwig_file, coordinates)	Extract per-base or binned pair values from a bigWig file for a set of genomic region.
hot_encoding_to_sequence(...)	Decode a one hot encoded sequence to a DNA sequence string.
one_hot_encode_sequence(sequence[, expand_dim])	One hot encode a DNA sequence.
fetch_sequences(regions[, genome, uppercase])	Fetch sequences from a genome file for a list of regions using pysam.
reverse_complement(sequence)	Perform reverse complement on either a one-hot encoded array or a (list of) DNA sequence string(s).
permute_model(model, new_input_shape)	Add a permutation layer to the input of a model to change the shape from (B, W, C) to (B, C, W) or vice versa.
setup_logging([log_level, log_file])	Set up loguru logging for the package.