Selector#
- class biotite.sequence.align.Selector(permutation: Permutation | None = None)[source]#
Bases:
Generic[S]Abstract base class for all k-mer subset selectors.
A selector reduces the number of k-mers obtained from a sequence by choosing a representative subset, while still ensuring that the same k-mers are selected from similar sequences. The criterion for selecting a k-mer depends on the concrete subclass.
- Parameters:
- permutationPermutation
If set, the k-mer order is permuted, i.e. the selection is based on the ordering of the sort keys from
Permutation.permute(), instead of the standard order of theKmerAlphabet.
- Attributes:
- permutationPermutation
The permutation.
- abstractmethod select(sequence, alphabet_check=True)#
Obtain all overlapping k-mers from a sequence and select a subset of them.
- Parameters:
- sequenceSequence
The sequence to select the k-mers from. Must be compatible with the selector’s k-mer alphabet.
- alphabet_checkbool, optional
If set to false, the compatibility between the alphabet of the sequence and the alphabet of the selector is not checked to gain additional performance.
- Returns:
- indicesndarray, dtype=np.uint32
The sequence indices where the selected k-mers start.
- kmersndarray, dtype=np.int64
The corresponding k-mer codes of the selected k-mers.
- abstractmethod select_from_kmers(kmers)#
Select a subset of the given k-mers.
- Parameters:
- kmersndarray, dtype=np.int64
The k-mer codes to select a subset from.
- Returns:
- indicesndarray, dtype=np.uint32
The indices in the input k-mer array of the selected k-mers.
- kmersndarray, dtype=np.int64
The corresponding k-mer codes of the selected k-mers.
