get_codes#

biotite.sequence.align.get_codes(alignment)[source]#

Get the sequence codes of the sequences in the alignment.

The codes are built from the trace: Instead of the indices of the aligned symbols (trace), the return value contains the corresponding symbol codes for each index. Gaps are still represented by -1.

Parameters:
alignmentAlignment

The alignment to get the sequence codes for.

Returns:
codesndarray, dtype=int, shape=(n,m)

The sequence codes for the alignment. The shape is (n,m) for n sequences and m alignment cloumn. The array uses -1 values for gaps.

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_codes(ali))
[[ 1  2  3  1  0  3 -1 -1]
 [-1 -1  3  1  0  3  2  1]]
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