mutcleaner.core.sequence#

Classes

`BaseSequence`(sequence[, alphabet, name, ...])	Base class for biological sequences
`DNASequence`(sequence[, alphabet, name, metadata])	DNA sequence with nucleotide validation
`ProteinSequence`(sequence[, alphabet, name, ...])	Protein sequence with amino acid validation
`RNASequence`(sequence[, alphabet, name, metadata])	RNA sequence with nucleotide validation

class mutcleaner.core.sequence.BaseSequence(sequence, alphabet=None, name=None, metadata=None)[source]#

Bases: ABC

Base class for biological sequences

Methods

`apply_mutation`(mutation)	Apply a mutation or set of mutations to the sequence and return a new sequence.
`default_alphabet`()	Subclasses may override this method to provide a default alphabet.
`get_subsequence`(start[, end])	get subsequence (0-indexed, inclusive)
`infer_mutation`(other)	Infer a mutation that leads to a specific sequence

apply_mutation(mutation)[source]#

Apply a mutation or set of mutations to the sequence and return a new sequence.

Parameters:

mutation (Union[BaseMutation, MutationSet, MutationSet[BaseMutation]]) – A single mutation or a set of mutations to apply

Return type:

TypeVar(SequenceType, bound= BaseSequence)

Returns:

A new sequence with the mutation(s) applied

Raises:

ValueError – If mutation position is invalid or mutation is incompatible
TypeError – If mutation type is not supported

classmethod default_alphabet()[source]#

Subclasses may override this method to provide a default alphabet.

By default, it returns None, indicating no default is provided and callers must pass alphabet explicitly.

Return type:: Optional[BaseAlphabet]

get_subsequence(start, end=None)[source]#

get subsequence (0-indexed, inclusive)

Return type:: TypeVar(SequenceType, bound= BaseSequence)

infer_mutation(other)[source]#

Infer a mutation that leads to a specific sequence

Return type:: MutationSet

class mutcleaner.core.sequence.DNASequence(sequence, alphabet=None, name=None, metadata=None)[source]#

Bases: BaseSequence

DNA sequence with nucleotide validation

Methods

`apply_mutation`(mutation)	Apply a mutation or set of mutations to the sequence and return a new sequence.
`default_alphabet`()	Subclasses may override this method to provide a default alphabet.
`get_subsequence`(start[, end])	get subsequence (0-indexed, inclusive)
`infer_mutation`(other)	Infer a mutation that leads to a specific sequence
`reverse_complement`()	Get reverse complement of DNA sequence
`transcribe`()	Transcribe DNA sequence into RNA sequence
`translate`([codon_table, start_at_first_met, ...])	Translate DNA sequence into amino acid sequence using this codon table.

classmethod default_alphabet()[source]#

Subclasses may override this method to provide a default alphabet.

By default, it returns None, indicating no default is provided and callers must pass alphabet explicitly.

Return type:: Optional[BaseAlphabet]

reverse_complement()[source]#

Get reverse complement of DNA sequence

Return type:: DNASequence

transcribe()[source]#

Transcribe DNA sequence into RNA sequence

Return type:: RNASequence

translate(codon_table=None, start_at_first_met=False, stop_at_stop_codon=False, require_mod3=True, start=None, end=None)[source]#

Translate DNA sequence into amino acid sequence using this codon table.

Parameters:

codon_table (Optional[CodonTable]) – Codon table to use for translation. If None, uses standard genetic code.
start_at_first_met (bool) – Start translation at the first start codon if found.
stop_at_stop_codon (bool) – Stop translation when a stop codon is encountered.
require_mod3 (bool) – Whether the sequence must be a multiple of 3 in length.
start (Optional[int]) – Custom 0-based start position. Overrides start_at_first_met.
end (Optional[int]) – Custom 0-based end position. Overrides stop_at_stop_codon.

Return type:

ProteinSequence

Returns:

Translated amino acid sequence.

class mutcleaner.core.sequence.ProteinSequence(sequence, alphabet=None, name=None, metadata=None)[source]#

Bases: BaseSequence

Protein sequence with amino acid validation

Methods

`apply_mutation`(mutation)	Apply a mutation or set of mutations to the sequence and return a new sequence.
`default_alphabet`()	Subclasses may override this method to provide a default alphabet.
`find_motif`(motif)	Find all positions where motif occurs (0-indexed)
`get_residue`(position)	Get amino acid at specific position (0-indexed)
`get_subsequence`(start[, end])	get subsequence (0-indexed, inclusive)
`infer_mutation`(other)	Infer a mutation that leads to a specific sequence

classmethod default_alphabet()[source]#

Subclasses may override this method to provide a default alphabet.

By default, it returns None, indicating no default is provided and callers must pass alphabet explicitly.

Return type:: Optional[BaseAlphabet]

find_motif(motif)[source]#

Find all positions where motif occurs (0-indexed)

Return type:: List[int]

get_residue(position)[source]#

Get amino acid at specific position (0-indexed)

Return type:: str

class mutcleaner.core.sequence.RNASequence(sequence, alphabet=None, name=None, metadata=None)[source]#

Bases: BaseSequence

RNA sequence with nucleotide validation

Methods

`apply_mutation`(mutation)	Apply a mutation or set of mutations to the sequence and return a new sequence.
`back_transcribe`()	Back-transcribe RNA sequence into DNA sequence
`default_alphabet`()	Subclasses may override this method to provide a default alphabet.
`get_subsequence`(start[, end])	get subsequence (0-indexed, inclusive)
`infer_mutation`(other)	Infer a mutation that leads to a specific sequence
`reverse_complement`()	Get reverse complement of RNA sequence
`translate`([codon_table, start_at_first_met, ...])	Translate RNA sequence into amino acid sequence using this codon table.

back_transcribe()[source]#

Back-transcribe RNA sequence into DNA sequence

Return type:: DNASequence

classmethod default_alphabet()[source]#

Subclasses may override this method to provide a default alphabet.

By default, it returns None, indicating no default is provided and callers must pass alphabet explicitly.

Return type:: Optional[BaseAlphabet]

reverse_complement()[source]#

Get reverse complement of RNA sequence

Return type:: RNASequence

translate(codon_table=None, start_at_first_met=False, stop_at_stop_codon=False, require_mod3=True, start=None, end=None)[source]#

Translate RNA sequence into amino acid sequence using this codon table.

Parameters:

codon_table (Optional[CodonTable]) – Codon table to use for translation. If None, uses standard genetic code.
start_at_first_met (bool) – Start translation at the first start codon if found.
stop_at_stop_codon (bool) – Stop translation when a stop codon is encountered.
require_mod3 (bool) – Whether the sequence must be a multiple of 3 in length.
start (Optional[int]) – Custom 0-based start position. Overrides start_at_first_met.
end (Optional[int]) – Custom 0-based end position. Overrides stop_at_stop_codon.

Return type:

ProteinSequence

Returns:

Translated amino acid sequence.