test_blast_101_search.py

import unittest
import blast_101_search as blast
import programme_settings

# Adapted from oficial Python unittest documentation: https://docs.python.org/3/library/unittest.html
# Python testing guide: https://realpython.com/python-testing/
# help from ChatGPT for structure and writing improved outputs.

class BlastCoreTests(unittest.TestCase):

    def setUp(self):
        # Use a protein sequence with valid residues
        query = "ACDEFGHIKLMNPQRSTVWY"
        programme_settings.settings["DEFAULT"]["query_sequence"] = query
        programme_settings.settings["BLAST"]["word_size"] = "4"
        programme_settings.settings["BLAST"]["tscore"] = "10"
        programme_settings.settings["BLAST"]["tscore_sim"] = "10"
        programme_settings.write()  # Persist the settings for the module

        # update values used by blast module match settings
        blast.qsequence = query.upper()
        blast.word_size = int(programme_settings.settings["BLAST"]["word_size"])
        blast.query_sequence = blast.tdict.create_word_dict(blast.qsequence)
        
    def test_blast_exact_match(self):
        '''BLAST search should find high scores for exact matches.'''
        print("\nRunning test: BLAST exact match... ", end="")
        target_seq = "ACDEFGHIKLMNPQRSTVWY"
        score = blast.process_blast(target_seq)
        self.assertGreater(score, 0, "Expected a non-zero score for matching sequence")
        print(f"PASSED: Exact match score = {score:.2f}")

    def test_blast_no_match(self):
        '''BLAST search should find zero score for no matching residues.'''
        print("\nRunning test: BLAST no match (invalid residues)... ", end="")
        target_seq = "ZZZZZZZZZZZZZZZZZZZZ"
        score = blast.process_blast(target_seq)
        self.assertEqual(score, 0, "Expected a zero score for non-matching sequence")
        print("PASSED: No match yielded score = 0")

    def test_sequence_shorter_than_wordsize(self):
        '''BLAST should return zero score for input shorter than word size.'''
        print("\nRunning test: BLAST with query shorter than word size... ", end="")
        target_seq = "PWA"  # Less than word_size=3
        score = blast.process_blast(target_seq)
        self.assertEqual(score, 0, "Expected score = 0 for sequence too short to match")
        print("PASSED: Sequence too short returned score = 0")
    
    def test_alignment_off_by_one_bug(self):
        '''Test alignment does not suffer from off-by-one errors.'''
        print("\nRunning test: BLAST alignment shifted by one residue... ", end="")
        query = "ACDEFGHIKLMNPQRSTVWY"
        # Same sequence shifted by one character should still yield a lower but non-zero score
        target = "CDEFGHIKLMNPQRSTVWYA"
        score_original = blast.process_blast(query)
        score_shifted = blast.process_blast(target)
        self.assertLess(score_shifted, score_original, "Off-by-one shifted sequence should have lower score than identical sequence, but not zero.")
        print(f"PASSED: Shifted match score = {score_shifted:.2f} < Exact = {score_original:.2f}")


if __name__ == "__main__":
    unittest.main()