biotite.sequence.align.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

get_codes

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']]