tidymut.core.sequence module
- class tidymut.core.sequence.BaseSequence(sequence: str, alphabet: BaseAlphabet, name: str | None = None, metadata: Dict | None = None)[source]
Bases:
ABC
Base class for biological sequences
- apply_mutation(mutation: BaseMutation | MutationSet | MutationSet[BaseMutation]) SequenceType [source]
Apply a mutation or set of mutations to the sequence and return a new sequence.
- Parameters:
mutation (Union[BaseMutation, CodonMutationSet, AminoAcidMutationSet]) – A single mutation or a set of mutations to apply
- Returns:
A new sequence with the mutation(s) applied
- Return type:
SequenceType
- Raises:
ValueError – If mutation position is invalid or mutation is incompatible
TypeError – If mutation type is not supported
- class tidymut.core.sequence.DNASequence(sequence: str, alphabet: DNAAlphabet | None = None, name: str | None = None, metadata: Dict | None = None)[source]
Bases:
BaseSequence
DNA sequence with nucleotide validation
- reverse_complement() DNASequence [source]
Get reverse complement of DNA sequence
- transcribe() RNASequence [source]
Transcribe DNA sequence into RNA sequence
- translate(codon_table: CodonTable | None = None, start_at_first_met: bool = False, stop_at_stop_codon: bool = False, require_mod3: bool = True, start: int | None = None, end: int | None = None) ProteinSequence [source]
Translate DNA sequence into amino acid sequence using this codon table.
- Parameters:
codon_table (Optional[CodonTable], default=None) – Codon table to use for translation. If None, uses standard genetic code.
start_at_first_met (bool, default=False) – Start translation at the first start codon if found.
stop_at_stop_codon (bool, default=False) – Stop translation when a stop codon is encountered.
require_mod3 (bool, default=True) – Whether the sequence must be a multiple of 3 in length.
start (Option[int], default=None) – Custom 0-based start position. Overrides start_at_first_met.
end (Option[int], default=None) – Custom 0-based end position. Overrides stop_at_stop_codon.
- Returns:
Translated amino acid sequence.
- Return type:
- class tidymut.core.sequence.ProteinSequence(sequence: str, alphabet: ProteinAlphabet | None = None, name: str | None = None, metadata: Dict | None = None)[source]
Bases:
BaseSequence
Protein sequence with amino acid validation
- class tidymut.core.sequence.RNASequence(sequence: str, alphabet: RNAAlphabet | None = None, name: str | None = None, metadata: Dict | None = None)[source]
Bases:
BaseSequence
RNA sequence with nucleotide validation
- back_transcribe() DNASequence [source]
Back-transcribe RNA sequence into DNA sequence
- reverse_complement() RNASequence [source]
Get reverse complement of RNA sequence
- translate(codon_table: CodonTable | None = None, start_at_first_met: bool = False, stop_at_stop_codon: bool = False, require_mod3: bool = True, start: int | None = None, end: int | None = None) ProteinSequence [source]
Translate RNA sequence into amino acid sequence using this codon table.
- Parameters:
codon_table (Optional[CodonTable], default=None) – Codon table to use for translation. If None, uses standard genetic code.
start_at_first_met (bool, default=False) – Start translation at the first start codon if found.
stop_at_stop_codon (bool, default=False) – Stop translation when a stop codon is encountered.
require_mod3 (bool, default=True) – Whether the sequence must be a multiple of 3 in length.
start (Option[int], default=None) – Custom 0-based start position. Overrides start_at_first_met.
end (Option[int], default=None) – Custom 0-based end position. Overrides stop_at_stop_codon.
- Returns:
Translated amino acid sequence.
- Return type: