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| """Tests for the backend-emitted MSA column statistics. | |
| The frontend renders these values verbatim; these tests pin the exact | |
| scientific semantics: matched = invariant column, mismatched = variable | |
| column with no gaps, gapped = column containing at least one gap. | |
| All runs are offline. | |
| """ | |
| from app.tools.alignment_stats import alignment_stats, parse_aligned_fasta | |
| class TestParseAlignedFasta: | |
| def test_returns_bodies_in_order(self): | |
| seqs = parse_aligned_fasta(">a\nAC-T\n>bb\nA-CT\n>c\nACT-") | |
| assert seqs == ["AC-T", "A-CT", "ACT-"] | |
| def test_ignores_whitespace_and_blank_lines(self): | |
| seqs = parse_aligned_fasta("\n>a\nA-C\nT\n \n>b\nAC-\nT\n") | |
| assert seqs == ["A-CT", "AC-T"] | |
| def test_empty_input(self): | |
| assert parse_aligned_fasta("") == [] | |
| assert parse_aligned_fasta(None) == [] | |
| class TestAlignmentStats: | |
| def test_identical_sequences(self): | |
| stats = alignment_stats(["ACDEFGHIK", "ACDEFGHIK"]) | |
| assert stats["length"] == 9 | |
| assert stats["matched"] == 9 | |
| assert stats["mismatched"] == 0 | |
| assert stats["gapped"] == 0 | |
| assert stats["total_gaps"] == 0 | |
| assert stats["identity_pct"] == 100.0 | |
| def test_single_gap_columns(self): | |
| stats = alignment_stats(["AC-T", "A-CT"]) | |
| assert stats["length"] == 4 | |
| assert stats["matched"] == 2 | |
| assert stats["gapped"] == 2 | |
| assert stats["total_gaps"] == 2 | |
| assert stats["mismatched"] == 0 | |
| assert round(stats["identity_pct"], 1) == 50.0 | |
| def test_mismatch_column_without_gaps(self): | |
| stats = alignment_stats(["ACD", "ACG"]) | |
| assert stats["length"] == 3 | |
| assert stats["matched"] == 2 | |
| assert stats["mismatched"] == 1 | |
| assert stats["gapped"] == 0 | |
| def test_trailing_gap_collapsing(self): | |
| stats = alignment_stats(["AC-T", "A-CT", "ACT-"]) | |
| assert stats["gapped"] == 3 | |
| assert stats["matched"] == 1 | |
| assert stats["mismatched"] == 0 | |
| assert stats["total_gaps"] == 3 | |
| def test_case_insensitive_matching(self): | |
| stats = alignment_stats(["ACD", "acd"]) | |
| assert stats["matched"] == 3 | |
| assert stats["identity_pct"] == 100.0 | |
| def test_empty_and_ragged_input(self): | |
| empty = alignment_stats([]) | |
| assert empty["length"] == 0 and empty["identity_pct"] == 0.0 | |
| ragged = alignment_stats(["ACD", "AC"]) | |
| assert ragged["length"] == 3 | |
| assert ragged["gapped"] == 1 |