""" Integration tests that exercise real ecosystem packages. These tests require the actual packages installed (biopython, scikit-bio). They are skipped when the packages are not available, but exercised in CI via the test_ecosystem job which installs kalign[all]. Biopython and scikit-bio test groups are independently skippable. """ import os import pytest import kalign # --------------------------------------------------------------------------- # Helpers # --------------------------------------------------------------------------- def _skip_no_biopython(): try: import Bio # noqa: F401 return False except ImportError: return True def _skip_no_skbio(): try: import skbio # noqa: F401 return False except ImportError: return True def _assert_alignment_valid(aligned, input_seqs): """Verify aligned sequences are a plausible alignment of the inputs.""" assert len(aligned) == len(input_seqs), ( f"Aligned count ({len(aligned)}) != input count ({len(input_seqs)})" ) # All aligned sequences must be the same length lengths = {len(s) for s in aligned} assert len(lengths) == 1, f"Inconsistent alignment lengths: {lengths}" aln_len = lengths.pop() # Alignment must be at least as long as the longest input max_input = max(len(s) for s in input_seqs) assert aln_len >= max_input # If inputs differ in length, at least one aligned seq must contain gaps if len({len(s) for s in input_seqs}) > 1: assert any("-" in s for s in aligned), "Inputs differ in length but no gaps in alignment" # Ungapped content must match the original sequences for orig, aln in zip(input_seqs, aligned): assert aln.replace("-", "") == orig # --------------------------------------------------------------------------- # Test data # --------------------------------------------------------------------------- DNA_SEQS = ["ATCGATCGATCG", "ATCGTCGATCG", "ATCGATCATCG"] DNA_IDS = ["seq1", "seq2", "seq3"] RNA_SEQS = ["AUCGAUCGAUCG", "AUCGUCGAUCG", "AUCGAUCAUCG"] PROTEIN_SEQS = [ "MKTAYIAKQRQISFVK", "MKTAYIAKQRQ", "MKTAYIAK", ] # Path to test FASTA data shipped with the project TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), "..", "data") TEST_FASTA = os.path.join(TEST_DATA_DIR, "BB11001.tfa") # --------------------------------------------------------------------------- # Biopython tests (skipped independently if Bio is not installed) # --------------------------------------------------------------------------- @pytest.mark.skipif(_skip_no_biopython(), reason="Biopython not installed") class TestBiopythonFormat: """Test fmt='biopython' with real Biopython.""" def test_align_biopython_format_dna(self): from Bio.Align import MultipleSeqAlignment result = kalign.align(DNA_SEQS, fmt="biopython", ids=DNA_IDS) assert isinstance(result, MultipleSeqAlignment) assert len(result) == len(DNA_SEQS) assert result[0].id == "seq1" assert result[1].id == "seq2" assert result[2].id == "seq3" # Verify actual alignment content aligned_strs = [str(r.seq) for r in result] _assert_alignment_valid(aligned_strs, DNA_SEQS) def test_align_biopython_format_protein(self): from Bio.Align import MultipleSeqAlignment result = kalign.align( PROTEIN_SEQS, seq_type="protein", fmt="biopython", ids=["p1", "p2", "p3"], ) assert isinstance(result, MultipleSeqAlignment) assert len(result) == len(PROTEIN_SEQS) aligned_strs = [str(r.seq) for r in result] _assert_alignment_valid(aligned_strs, PROTEIN_SEQS) def test_align_biopython_auto_ids(self): from Bio.Align import MultipleSeqAlignment result = kalign.align(DNA_SEQS, fmt="biopython") assert isinstance(result, MultipleSeqAlignment) assert result[0].id == "seq0" @pytest.mark.skipif(_skip_no_biopython(), reason="Biopython not installed") class TestIORead: """Test kalign.io read functions with real Biopython.""" def test_read_fasta(self): sequences = kalign.io.read_fasta(TEST_FASTA) assert isinstance(sequences, list) assert len(sequences) > 0 assert all(isinstance(s, str) for s in sequences) assert all(len(s) > 0 for s in sequences) def test_read_sequences(self): sequences, ids = kalign.io.read_sequences(TEST_FASTA) assert len(sequences) == len(ids) assert len(sequences) > 0 assert all(len(s) > 0 for s in sequences) assert all(len(i) > 0 for i in ids) @pytest.mark.skipif(_skip_no_biopython(), reason="Biopython not installed") class TestIOWrite: """Test kalign.io write functions with real Biopython.""" @pytest.fixture def aligned(self): return kalign.align(DNA_SEQS) def test_write_fasta_roundtrip(self, aligned, tmp_path): out = tmp_path / "out.fasta" kalign.io.write_fasta(aligned, str(out), ids=DNA_IDS) read_back = kalign.io.read_fasta(str(out)) assert read_back == aligned def test_write_clustal(self, aligned, tmp_path): from Bio import AlignIO out = tmp_path / "out.aln" kalign.io.write_clustal(aligned, str(out), ids=DNA_IDS) aln = AlignIO.read(str(out), "clustal") assert len(aln) == len(aligned) assert aln.get_alignment_length() == len(aligned[0]) # Verify content matches for orig, record in zip(aligned, aln): assert str(record.seq) == orig def test_write_stockholm(self, aligned, tmp_path): from Bio import AlignIO out = tmp_path / "out.sto" kalign.io.write_stockholm(aligned, str(out), ids=DNA_IDS) aln = AlignIO.read(str(out), "stockholm") assert len(aln) == len(aligned) assert aln.get_alignment_length() == len(aligned[0]) for orig, record in zip(aligned, aln): assert str(record.seq) == orig def test_write_phylip(self, aligned, tmp_path): from Bio import AlignIO out = tmp_path / "out.phy" kalign.io.write_phylip(aligned, str(out), ids=DNA_IDS) aln = AlignIO.read(str(out), "phylip-sequential") assert len(aln) == len(aligned) for orig, record in zip(aligned, aln): assert str(record.seq) == orig # --------------------------------------------------------------------------- # scikit-bio tests (skipped independently if skbio is not installed) # --------------------------------------------------------------------------- @pytest.mark.skipif(_skip_no_skbio(), reason="scikit-bio not installed") class TestSkbioFormat: """Test fmt='skbio' with real scikit-bio.""" def test_align_skbio_format_dna(self): import skbio result = kalign.align(DNA_SEQS, seq_type="dna", fmt="skbio", ids=DNA_IDS) assert isinstance(result, skbio.TabularMSA) assert len(result) == len(DNA_SEQS) assert all(isinstance(seq, skbio.DNA) for seq in result) # Verify alignment content aligned_strs = [str(seq) for seq in result] _assert_alignment_valid(aligned_strs, DNA_SEQS) def test_align_skbio_format_rna(self): import skbio result = kalign.align(RNA_SEQS, seq_type="rna", fmt="skbio") assert isinstance(result, skbio.TabularMSA) assert len(result) == len(RNA_SEQS) assert all(isinstance(seq, skbio.RNA) for seq in result) aligned_strs = [str(seq) for seq in result] _assert_alignment_valid(aligned_strs, RNA_SEQS) def test_align_skbio_format_protein(self): import skbio result = kalign.align( PROTEIN_SEQS, seq_type="protein", fmt="skbio", ids=["p1", "p2", "p3"] ) assert isinstance(result, skbio.TabularMSA) assert len(result) == len(PROTEIN_SEQS) assert all(isinstance(seq, skbio.Protein) for seq in result) aligned_strs = [str(seq) for seq in result] _assert_alignment_valid(aligned_strs, PROTEIN_SEQS) def test_align_skbio_auto_detect_dna(self): """AUTO seq_type should infer DNA and produce skbio.DNA objects.""" import skbio result = kalign.align(DNA_SEQS, fmt="skbio") assert all(isinstance(seq, skbio.DNA) for seq in result) def test_align_skbio_auto_detect_protein(self): """AUTO seq_type should infer Protein and produce skbio.Protein objects.""" import skbio result = kalign.align(PROTEIN_SEQS, fmt="skbio") assert all(isinstance(seq, skbio.Protein) for seq in result) def test_align_skbio_metadata(self): import skbio result = kalign.align(DNA_SEQS, seq_type="dna", fmt="skbio", ids=DNA_IDS) assert result[0].metadata["id"] == "seq1" assert result[1].metadata["id"] == "seq2" assert result[2].metadata["id"] == "seq3"