def test_calculate_percent_identity(self):
"""
Test the calculate percent identity function
"""
cigar_string="100S84M16S"
md_field="MD:Z:27A5G2T6G4T1A6T2C0A7A1A0A0C0G1G1A5"
expected_identity= 100.0 * ( 68 / 84.0 )
identity, alignment_length =nucleotide.calculate_percent_identity(cigar_string,md_field)
self.assertEqual(identity, expected_identity)
def test_calculate_percent_identity_simple_md_field(self):
"""
Test the calculate percent identity function
Test with a simple md field where all bases match
"""
cigar_string="100S84M16S"
md_field="MD:Z:84"
expected_identity= 100.0 * ( 84 / 84.0 )
identity, alignment_length=nucleotide.calculate_percent_identity(cigar_string,md_field)
self.assertEqual(identity, expected_identity)
def test_calculate_percent_identity_two_match_mismatch_identifiers(self):
"""
Test the calculate percent identity function
Test cigar string with the two match and mistmatch identifiers (X and =)
"""
cigar_string="100I84M1X2=2D"
md_field="MD:Z:27A5G2T6G4T1A6T2C0A7A1A0A0C0G1G1A5"
expected_identity= 100.0 * ( 68 / 189.0 )
identity, alignment_length =nucleotide.calculate_percent_identity(cigar_string,md_field)
self.assertEqual(identity, expected_identity)
def test_calculate_percent_identity_insert_delete(self):
"""
Test the calculate percent identity function
Test cigar string with insert and deletes
"""
cigar_string="100I84M2D"
md_field="MD:Z:27A5G2T6G4T1A6T2C0A7A1A0A0C0G1G1A5"
expected_identity= 100.0 * ( 68 / 186.0 )
identity, alignment_length =nucleotide.calculate_percent_identity(cigar_string,md_field)
self.assertEqual(identity, expected_identity)
def test_calculate_percent_identity_missing_md_field(self):
"""
Test the calculate percent identity function
Test with an empty md field
"""
cigar_string="100S84M16S"
md_field=""
expected_identity=0.0
identity, alignment_length=nucleotide.calculate_percent_identity(cigar_string,md_field)
self.assertEqual(identity, expected_identity)
def test_calculate_percent_identity_missing_cigar_identifier(self):
"""
Test the calculate percent identity function
Test with a cigar string that does not have the match/mismatch identifier
"""
cigar_string="*"
md_field="MD:Z:84"
expected_identity=0.0
identity, alignment_length=nucleotide.calculate_percent_identity(cigar_string,md_field)
self.assertEqual(identity, expected_identity)