get_symbols
#
- biotite.sequence.align.get_symbols(alignment)[source]#
Similar to
get_codes()
, but contains the decoded symbols instead of codes. Gaps are still represented by None values.- Parameters:
- alignmentAlignment
The alignment to get the symbols for.
- Returns:
- symbolslist of list
The nested list of symbols.
See also
Examples
>>> seq1 = NucleotideSequence("CGTCAT") >>> seq2 = NucleotideSequence("TCATGC") >>> matrix = SubstitutionMatrix.std_nucleotide_matrix() >>> ali = align_optimal(seq1, seq2, matrix)[0] >>> print(ali) CGTCAT-- --TCATGC >>> print(get_symbols(ali)) [['C', 'G', 'T', 'C', 'A', 'T', None, None], [None, None, 'T', 'C', 'A', 'T', 'G', 'C']]
Gallery#
Plot epitope mapping data onto protein sequence alignments
Plot epitope mapping data onto protein sequence alignments