"""Tests for alignment operations."""
from biopython_mcp.alignment import calculate_alignment_score, pairwise_align
class TestPairwiseAlign:
"""Tests for pairwise_align function."""
def test_global_alignment_identical(self) -> None:
"""Test global alignment of identical sequences."""
result = pairwise_align("ATCG", "ATCG", mode="global")
assert result["success"] is True
assert result["mode"] == "global"
assert result["score"] > 0
def test_global_alignment_different(self) -> None:
"""Test global alignment of different sequences."""
result = pairwise_align("ATCG", "TTTT", mode="global")
assert result["success"] is True
assert result["mode"] == "global"
def test_local_alignment(self) -> None:
"""Test local alignment."""
result = pairwise_align("ATCGATCG", "ATCG", mode="local")
assert result["success"] is True
assert result["mode"] == "local"
def test_custom_scoring(self) -> None:
"""Test alignment with custom scoring."""
result = pairwise_align("ATCG", "ATCG", match_score=5.0, mismatch_score=-2.0, gap_open=-3.0)
assert result["success"] is True
assert result["parameters"]["match_score"] == 5.0
class TestCalculateAlignmentScore:
"""Tests for calculate_alignment_score function."""
def test_alignment_score_blosum62(self) -> None:
"""Test alignment scoring with BLOSUM62."""
alignment = ">seq1\nACDEFG\n>seq2\nACDEFG"
result = calculate_alignment_score(alignment, matrix_name="BLOSUM62")
assert result["success"] is True
assert result["matrix_used"] == "BLOSUM62"
def test_alignment_score_invalid_matrix(self) -> None:
"""Test alignment scoring with invalid matrix."""
alignment = ">seq1\nACDEFG\n>seq2\nACDEFG"
result = calculate_alignment_score(alignment, matrix_name="INVALID")
assert result["success"] is False
assert "available_matrices" in result
def test_alignment_score_statistics(self) -> None:
"""Test alignment statistics calculation."""
alignment = "ATCG\nATCG"
result = calculate_alignment_score(alignment)
assert result["success"] is True
assert "statistics" in result
assert "matches" in result["statistics"]
