alphabet#

CharAlphabet(chars[, gap, missing])

representing fundamental monomer character sets.

KmerAlphabet(words, monomers, k[, gap, missing])

k-mer alphabet represents complete non-monomer alphabets

SenseCodonAlphabet(words, monomers[, gap])

represents the sense-codons of a GeneticCode

PhredEncoding(*values)

fastq quality score encoding schemes

bytes_to_array(chars, dtype[, delete, dest])

wrapper around convert_alphabet.

make_qual_converter([scoring_scheme])

make a converter from fastq quality ASCII bytes to numpy uint8 scores.

make_text_to_array_converter(alphabet[, delete])

make a converter from text bytes to alphabet indices.