"""Tests for sequence operations."""
from biopython_mcp.sequence import (
calculate_gc_content,
find_motif,
reverse_complement,
transcribe_dna,
translate_sequence,
)
class TestTranslateSequence:
"""Tests for translate_sequence function."""
def test_translate_simple_dna(self) -> None:
"""Test translation of a simple DNA sequence."""
result = translate_sequence("ATGGCCATTGTAATGGGCCGC")
assert result["success"] is True
assert result["protein_sequence"] == "MAIVMGR"
assert result["protein_length"] == 7
def test_translate_with_stop_codon(self) -> None:
"""Test translation stopping at stop codon."""
result = translate_sequence("ATGTAAGCC", to_stop=True)
assert result["success"] is True
assert result["protein_length"] == 1
def test_translate_invalid_sequence(self) -> None:
"""Test translation with invalid characters."""
result = translate_sequence("ATGXYZ")
assert result["success"] is False
assert "error" in result
class TestReverseComplement:
"""Tests for reverse_complement function."""
def test_reverse_complement_simple(self) -> None:
"""Test reverse complement of simple sequence."""
result = reverse_complement("ATCG")
assert result["success"] is True
assert result["reverse_complement"] == "CGAT"
def test_reverse_complement_longer(self) -> None:
"""Test reverse complement of longer sequence."""
result = reverse_complement("ATGGCCATTGTAATGGGCCGC")
assert result["success"] is True
assert len(result["reverse_complement"]) == 21
class TestTranscribeDNA:
"""Tests for transcribe_dna function."""
def test_transcribe_dna_to_rna(self) -> None:
"""Test DNA to RNA transcription."""
result = transcribe_dna("ATCG")
assert result["success"] is True
assert result["output_sequence"] == "AUCG"
assert result["operation"] == "transcription"
def test_reverse_transcribe_rna_to_dna(self) -> None:
"""Test RNA to DNA reverse transcription."""
result = transcribe_dna("AUCG", reverse=True)
assert result["success"] is True
assert result["output_sequence"] == "ATCG"
assert result["operation"] == "reverse_transcription"
class TestCalculateGCContent:
"""Tests for calculate_gc_content function."""
def test_gc_content_50_percent(self) -> None:
"""Test GC content calculation for 50% GC."""
result = calculate_gc_content("ATGC")
assert result["success"] is True
assert result["gc_content_percent"] == 50.0
def test_gc_content_high(self) -> None:
"""Test GC content calculation for high GC."""
result = calculate_gc_content("GGCC")
assert result["success"] is True
assert result["gc_content_percent"] == 100.0
def test_gc_content_counts(self) -> None:
"""Test nucleotide counts."""
result = calculate_gc_content("ATGC")
assert result["nucleotide_counts"]["A"] == 1
assert result["nucleotide_counts"]["T"] == 1
assert result["nucleotide_counts"]["G"] == 1
assert result["nucleotide_counts"]["C"] == 1
class TestFindMotif:
"""Tests for find_motif function."""
def test_find_motif_single_occurrence(self) -> None:
"""Test finding a motif with single occurrence."""
result = find_motif("ATGCATGC", "ATG")
assert result["success"] is True
assert result["occurrences"] == 2
assert result["positions"] == [0, 4]
def test_find_motif_no_occurrence(self) -> None:
"""Test finding a motif with no occurrence."""
result = find_motif("ATGC", "TTT")
assert result["success"] is True
assert result["occurrences"] == 0
assert result["positions"] == []
def test_find_motif_overlapping(self) -> None:
"""Test finding overlapping motifs."""
result = find_motif("AAAA", "AA", overlapping=True)
assert result["success"] is True
assert result["occurrences"] == 3
def test_find_motif_non_overlapping(self) -> None:
"""Test finding non-overlapping motifs."""
result = find_motif("AAAA", "AA", overlapping=False)
assert result["success"] is True
assert result["occurrences"] == 2
