mutcleaner.core.alphabet#

Classes

BaseAlphabet(letters, name)

Base class for biological alphabets

DNAAlphabet([include_ambiguous])

DNA alphabet (A, T, C, G)

ProteinAlphabet([include_stop, ...])

Protein alphabet (20 standard amino acids + stop codon)

RNAAlphabet([include_ambiguous])

RNA alphabet (A, U, C, G)
class mutcleaner.core.alphabet.BaseAlphabet(letters, name)[source]#

Bases: ABC

Base class for biological alphabets

Methods

get_invalid_chars(sequence)

Get set of invalid characters in sequence

is_valid_char(char)

Check if character is valid in this alphabet

is_valid_sequence(sequence)

Check if entire sequence is valid

validate_sequence(sequence)

Validate sequence and raise error if invalid
get_invalid_chars(sequence)[source]#

Get set of invalid characters in sequence

Return type:

Set[str]

is_valid_char(char)[source]#

Check if character is valid in this alphabet

Return type:

bool

is_valid_sequence(sequence)[source]#

Check if entire sequence is valid

Return type:

bool

validate_sequence(sequence)[source]#

Validate sequence and raise error if invalid

Return type:

str

class mutcleaner.core.alphabet.DNAAlphabet(include_ambiguous=False)[source]#

Bases: BaseAlphabet

DNA alphabet (A, T, C, G)

Methods

get_invalid_chars(sequence)

Get set of invalid characters in sequence

is_valid_char(char)

Check if character is valid in this alphabet

is_valid_sequence(sequence)

Check if entire sequence is valid

validate_sequence(sequence)

Validate sequence and raise error if invalid
class mutcleaner.core.alphabet.ProteinAlphabet(include_stop=True, include_ambiguous=False)[source]#

Bases: BaseAlphabet

Protein alphabet (20 standard amino acids + stop codon)

Methods

get_invalid_chars(sequence)

Get set of invalid characters in sequence

get_one_letter_code(three_letter[, strict])

Convert three-letter to one-letter amino acid code

get_three_letter_code(one_letter[, strict])

Convert one-letter to three-letter amino acid code

is_valid_char(char)

Check if character is valid in this alphabet

is_valid_sequence(sequence)

Check if entire sequence is valid

validate_sequence(sequence)

Validate sequence and raise error if invalid
get_one_letter_code(three_letter, strict=True)[source]#

Convert three-letter to one-letter amino acid code

Return type:

str

get_three_letter_code(one_letter, strict=True)[source]#

Convert one-letter to three-letter amino acid code

Return type:

str

class mutcleaner.core.alphabet.RNAAlphabet(include_ambiguous=False)[source]#

Bases: BaseAlphabet

RNA alphabet (A, U, C, G)

Methods

get_invalid_chars(sequence)

Get set of invalid characters in sequence

is_valid_char(char)

Check if character is valid in this alphabet

is_valid_sequence(sequence)

Check if entire sequence is valid

validate_sequence(sequence)

Validate sequence and raise error if invalid