Utilities: utils

General utility functions used across CREsted.

Functions

EnhancerOptimizer(*args, **kwargs)	(Alias function for the) class to optimize the mutated sequence based on the original prediction.
calculate_nucleotide_distribution(input[, ...])	Calculate the nucleotide distribution of a genome in a set of regions or sequences.
derive_intermediate_sequences(*args, **kwargs)	Use derive_intermediate_sequences() instead, this alias is deprecated.
fetch_sequences(regions[, genome, uppercase])	Fetch sequences from a genome file for a list of regions using pysam.
flip_region_strand(region)	Reverse the strand of a region strand or tuple.
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.
parse_region(region)	Parse a region string or tuple, returning a consistent (chr, start, end, strand) tuple.
read_bigwig_region(bigwig_file, coordinates)	Extract per-base or binned pair values from a bigWig file for a set of genomic region.
reverse_complement(sequence)	Perform reverse complement on either a one-hot encoded array or a (list of) DNA sequence string(s).
setup_logging([log_level, log_file])	Set up loguru logging for the package.