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"""
Edge case tests for Kalign Python package.
"""
import pytest
import kalign
class TestEdgeCases:
"""Test unusual inputs and boundary conditions."""
def test_identical_sequences(self):
"""Test alignment of identical sequences."""
identical = ["ATCGATCG"] * 3
aligned = kalign.align(identical, seq_type="dna")
assert len(aligned) == 3
# All should be identical (no gaps needed)
assert all(seq == aligned[0] for seq in aligned)
def test_very_short_sequences(self):
"""Test very short sequences."""
short_seqs = ["A", "T", "G"]
aligned = kalign.align(short_seqs, seq_type="dna")
assert len(aligned) == 3
assert all(len(seq) >= 1 for seq in aligned)
def test_very_different_lengths(self):
"""Test sequences with very different lengths."""
diff_lengths = ["A", "ATCGATCGATCGATCG", "ATCG"]
aligned = kalign.align(diff_lengths, seq_type="dna")
assert len(aligned) == 3
assert all(len(seq) == len(aligned[0]) for seq in aligned)
def test_single_character_sequences(self):
"""Test single character sequences."""
single_chars = ["A", "T", "C", "G"]
aligned = kalign.align(single_chars, seq_type="dna")
assert len(aligned) == 4
def test_repetitive_sequences(self):
"""Test highly repetitive sequences."""
repetitive = ["AAAAAAA", "TTTTTTT", "AAAAAAA"]
aligned = kalign.align(repetitive, seq_type="dna")
assert len(aligned) == 3
def test_mixed_case_sequences(self, mixed_case):
"""Test mixed case handling."""
aligned = kalign.align(mixed_case, seq_type="dna")
assert len(aligned) == len(mixed_case)
def test_large_sequence_count(self):
"""Test with many sequences."""
# Use valid DNA characters only - create variation with different bases
base_patterns = ["ATCG", "TACG", "GATC", "CGTA", "TGCA", "ACGT", "GCTA", "CTAG"]
many_seqs = []
for i in range(20):
pattern = base_patterns[i % len(base_patterns)]
# Add length variation with valid DNA bases
suffix = "A" * (i % 4) # Add 0-3 A's for length variation
many_seqs.append(f"{pattern}{suffix}TG")
aligned = kalign.align(many_seqs, seq_type="dna")
assert len(aligned) == 20
assert all(len(seq) == len(aligned[0]) for seq in aligned)
def test_ambiguous_nucleotides(self):
"""Test sequences with ambiguous nucleotides."""
ambiguous = ["ATCGN", "ATCGY", "ATCGR"]
# Use auto-detection since ambiguous nucleotides might be detected as protein
try:
aligned = kalign.align(ambiguous) # Let kalign auto-detect the type
assert len(aligned) == 3
# Should handle gracefully with auto-detection
except (ValueError, RuntimeError):
# Some ambiguous characters might still cause issues
pass
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