Harrison
b8fa4b5208
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43 lines
1.5 KiB
Python
43 lines
1.5 KiB
Python
from Bio.Align import PairwiseAligner, substitution_matrices
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from bmlsa.datatypes import AlignedSequence
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from bmlsa.exceptions import UnexpectedAlignmentResult
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def protein_align_many_to_one_ssw(sequence: str, queries: dict[str, AlignedSequence]):
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annotation_pairs = {}
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aligner = PairwiseAligner()
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aligner.mode = "local"
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aligner.substitution_matrix = substitution_matrices.load("BLOSUM62")
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aligner.extend_gap_score = -1
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aligner.open_gap_score = -11
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for id, query in queries.items():
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try:
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alignments = aligner.align(sequence, query.sequence)
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except ValueError:
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continue
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if len(alignments) > 1:
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raise UnexpectedAlignmentResult(
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"More than one alignment resulted from a single query."
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)
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for alignment in alignments:
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score, query_aligned = (alignment.score, alignment.aligned[0][0])
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aligned_start, aligned_end = query_aligned
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annotation_pairs[id] = AlignedSequence(
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id,
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query.sequence,
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query.name,
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query.description,
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query.start,
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query.end,
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query.score,
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), AlignedSequence(
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id,
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alignment.query,
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query.name,
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query.description,
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int(aligned_start) + 1,
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aligned_end,
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score,
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)
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return annotation_pairs
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