SimilarityRule
#
- class biotite.sequence.align.SimilarityRule[source]#
Bases:
object
This is the abstract base class for all similarity rules. A
SimilarityRule
calculates all similar k-mers for a given k-mer, while the definition of similarity depends on the derived class.- abstract similar_kmers(kmer_alphabet, kmer)#
Calculate all similar k-mers for a given k-mer.
- Parameters:
- kmer_alphabetKmerAlphabet
The reference k-mer alphabet to select the k-mers from.
- kmerint
The symbol code for the k-mer to find similars for.
- Returns:
- similar_kmersndarray, dtype=np.int64
The symbol codes for all similar k-mers.
Notes
The implementations in derived classes must ensure that the returned array
contains no duplicates and
includes the input kmer itself.