tidymut.core.alphabet module

class tidymut.core.alphabet.BaseAlphabet(letters: Set[str], name: str)[source]

Bases: ABC

Base class for biological alphabets

get_invalid_chars(sequence: str) Set[str][source]

Get set of invalid characters in sequence

is_valid_char(char: str) bool[source]

Check if character is valid in this alphabet

is_valid_sequence(sequence: str) bool[source]

Check if entire sequence is valid

validate_sequence(sequence: str) str[source]

Validate sequence and raise error if invalid

class tidymut.core.alphabet.DNAAlphabet(include_ambiguous: bool = False)[source]

Bases: BaseAlphabet

DNA alphabet (A, T, C, G)

class tidymut.core.alphabet.ProteinAlphabet(include_stop: bool = True, include_ambiguous: bool = False)[source]

Bases: BaseAlphabet

Protein alphabet (20 standard amino acids + stop codon)

get_one_letter_code(three_letter: str, strict: bool = True) str[source]

Convert three-letter to one-letter amino acid code

get_three_letter_code(one_letter: str, strict: bool = True) str[source]

Convert one-letter to three-letter amino acid code

class tidymut.core.alphabet.RNAAlphabet(include_ambiguous: bool = False)[source]

Bases: BaseAlphabet

RNA alphabet (A, U, C, G)