def get_alignment(cls, seq1: str, seq2: str, local: bool = True):
"""
Generate an alignment between two sequences
Parameters
----------
seq1: str
The first sequence to be aligned
seq1: str
The second sequence to be aligned
local: bool
If false, a global alignment is performed
(based on the Needleman-Wunsch algorithm),
otherwise a local alignment is performed
(based on the Smith–Waterman algorithm).
(Default: True)
Returns
-------
Alignment
"""
import biotite.sequence as seq
import biotite.sequence.align as align
import numpy as np
# create the default matrix
# TODO add more options for the choice of matrix
matrix = align.SubstitutionMatrix.std_protein_matrix()
alignments = align.align_optimal(
seq.ProteinSequence(seq1),
seq.ProteinSequence(seq2),
matrix,
local=local,
)
alignment = alignments[0]
score = alignment.score
seq_identity = align.get_sequence_identity(alignment)
symbols = align.get_symbols(alignment)
codes = align.get_codes(alignment)
return cls(
alignment=alignment,
metadata={
"score": score,
"sequence_identity": seq_identity,
"symbols": symbols,
"codes": codes,
},
)
def test_conversion_to_symbols():
"""
Test conversion of alignments to strings.
"""
seq_str1 = "HAKLPRDD--WKL--"
seq_str2 = "HA--PRDDADWKLHH"
seq_str3 = "HA----DDADWKLHH"
seq_strings = [seq_str1, seq_str2, seq_str3]
sequences = [seq.ProteinSequence(seq_str.replace("-",""))
for seq_str in seq_strings]
trace = align.Alignment.trace_from_strings(seq_strings)
alignment = align.Alignment(sequences, trace, score=None)
# Test the conversion bach to strings of symbols
symbols = align.get_symbols(alignment)
symbols = ["".join([sym if sym is not None else "-" for sym in sym_list])
for sym_list in symbols]
assert symbols == seq_strings
########################################################################
# If you are interested in more advanced visualization examples, have a
# look at the :doc:`example gallery <../examples/gallery/index>`.
#
# You can also do some simple analysis on these objects, like
# determining the sequence identity or calculating the score.
# For further custom analysis, it can be convenient to have directly the
# aligned symbos codes instead of the trace.
alignment = alignments[0]
print("Score: ", alignment.score)
print("Recalculated score:", align.score(alignment, matrix=matrix))
print("Sequence identity:", align.get_sequence_identity(alignment))
print("Symbols:")
print(align.get_symbols(alignment))
print("symbols codes:")
print(align.get_codes(alignment))
########################################################################
#
# .. currentmodule:: biotite.sequence.io.fasta
#
# You may ask, why should you recalculate the score, when the score has
# already been directly calculated via :func:`align_optimal()`.
# The answer is, that you might load an alignment from an external
# alignment program as FASTA file using :func:`get_alignment()`.
#
# .. currentmodule:: biotite.sequence.align
#
# If you want to perform a multiple sequence alignment, have a look at
