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| """Alignment column statistics — single backend implementation. | |
| This is the authoritative source for the MSA summary metrics that the | |
| frontend renders. The frontend must not recompute scientific numbers; it | |
| renders the values emitted here (the CLUSTAL-style display symbols stay a | |
| pure presentation concern). | |
| """ | |
| from __future__ import annotations | |
| GAP_CHARS = {"-", "."} | |
| # The scientific summary classifies columns exactly as the old client helper did: | |
| # matched — every non-gap residue identical (invariant column) | |
| # gapped — at least one gap character present | |
| # mismatched — >= 2 distinct residues and no gaps (variable column) | |
| def alignment_stats(seqs: list[str]) -> dict: | |
| """Column-wise summary of an already-aligned set of equal-length strings.""" | |
| empty = { | |
| "length": 0, | |
| "matched": 0, | |
| "mismatched": 0, | |
| "gapped": 0, | |
| "total_gaps": 0, | |
| "identity_pct": 0.0, | |
| } | |
| if not seqs: | |
| return empty | |
| length = max(len(s) for s in seqs) | |
| if length == 0: | |
| return empty | |
| matched = 0 | |
| mismatched = 0 | |
| gapped = 0 | |
| total_gaps = 0 | |
| for i in range(length): | |
| distinct: set[str] = set() | |
| col_has_gap = False | |
| for s in seqs: | |
| c = (s[i] if i < len(s) else "-").upper() | |
| if c in GAP_CHARS: | |
| col_has_gap = True | |
| total_gaps += 1 | |
| else: | |
| distinct.add(c) | |
| if col_has_gap: | |
| gapped += 1 | |
| elif len(distinct) <= 1: | |
| matched += 1 | |
| else: | |
| mismatched += 1 | |
| return { | |
| "length": length, | |
| "matched": matched, | |
| "mismatched": mismatched, | |
| "gapped": gapped, | |
| "total_gaps": total_gaps, | |
| "identity_pct": round(matched / length * 100, 1) if length else 0.0, | |
| } | |
| def parse_aligned_fasta(fasta: str) -> list[str]: | |
| """Return the aligned sequence bodies (lowercased headers removed, gaps kept).""" | |
| if not fasta: | |
| return [] | |
| seqs: list[str] = [] | |
| current = "" | |
| for line in (fasta or "").splitlines(): | |
| t = line.strip() | |
| if t.startswith(">"): | |
| if current: | |
| seqs.append(current) | |
| current = "" | |
| elif t: | |
| current += t | |
| if current: | |
| seqs.append(current) | |
| return seqs |