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"""
Unit tests for sequence validation functions.
"""
import unittest
from Bio.SeqUtils.ProtParam import ProteinAnalysis
from modules.validate_sequences import SequenceValidator
class TestSequenceValidator(unittest.TestCase):
def setUp(self):
# Test sequences with known properties
self.test_sequences = {
"acidic": "DDDEEEDDEE", # Should have low pI
"basic": "KKRRKKKRKR", # Should have high pI
"neutral": "GGGAAAGGG", # Should have middle pI
"mixed": "DEDKRKDEKR" # Should have intermediate pI
}
def test_pi_calculation(self):
"""Test that pI calculations match BioPython's results."""
for name, seq in self.test_sequences.items():
validator = SequenceValidator(seq)
our_properties = validator.calculate_properties()
our_pi = our_properties["pI"]
biopython_analysis = ProteinAnalysis(seq)
biopython_pi = biopython_analysis.isoelectric_point()
print(f"\nTesting {name} sequence:")
print(f"Sequence: {seq}")
print(f"Our pI: {our_pi}")
print(f"BioPython pI: {biopython_pi}")
print(f"Charge at pH 7: {validator.charge_at_ph(7.0)}")
print(f"BioPython charge at pH 7: {biopython_analysis.charge_at_pH(7.0)}")
self.assertAlmostEqual(
our_pi,
biopython_pi,
places=1,
msg=f"pI calculation failed for {name} sequence"
)
def test_gravy_calculation(self):
"""Test GRAVY calculations."""
hydrophobic = "ILVAAA" # Should have positive GRAVY
hydrophilic = "RKDENN" # Should have negative GRAVY
validator_hydrophobic = SequenceValidator(hydrophobic)
validator_hydrophilic = SequenceValidator(hydrophilic)
gravy_hydrophobic = validator_hydrophobic.calculate_properties()["GRAVY"]
gravy_hydrophilic = validator_hydrophilic.calculate_properties()["GRAVY"]
self.assertGreater(gravy_hydrophobic, 0)
self.assertLess(gravy_hydrophilic, 0)
if __name__ == '__main__':
unittest.main() |