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Replace pairwise2 with PairwiseAligner #37

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merged 3 commits into from
Nov 21, 2024
Merged

Replace pairwise2 with PairwiseAligner #37

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e06cf6f
Replace pairwise2 with PairwiseAligner
Ulthran Oct 18, 2024
313db9e
Include dashes in aligner formatting
Ulthran Oct 18, 2024
b635e82
Access alignemnt results directly from object
Ulthran Nov 20, 2024
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27 changes: 13 additions & 14 deletions unassigner/align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
import os.path
import subprocess
import tempfile
from Bio import pairwise2
from Bio.Align import PairwiseAligner

from unassigner.parse import write_fasta, parse_fasta
from unassigner.alignment import AlignedPair
Expand Down Expand Up @@ -261,16 +261,15 @@ def _get_subject_seq(self, subject_id):


def align_semiglobal(qseq, sseq):
alignment = pairwise2.align.globalms(
sseq,
qseq,
5,
-4,
-10,
-0.5, # match, mismatch, gapopen, gapextend
penalize_end_gaps=False,
one_alignment_only=True,
)
subj_seq = alignment[0][0]
query_seq = alignment[0][1]
return query_seq, subj_seq
aligner = PairwiseAligner()
aligner.mode = "global"
aligner.match_score = 5
aligner.mismatch_score = -4
aligner.open_gap_score = -10
aligner.extend_gap_score = -0.5
aligner.end_open_gap_score = 0
aligner.end_extend_gap_score = 0
alignments = aligner.align(sseq, qseq)
alignment = alignments[0]

return alignment[1], alignment[0]
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