def test_Two_Insertions_Consecutive(self):
# Two insertions at position 1 and 2.
data = "T[-/A][-/G]GACACGTACGT"
parser = SnpSequence(data)
snps = parser.snps()
expected = [Snp('.1insA'), Snp('.2insG')]
self.assertEqual(snps, expected)
def test_One_Insertion(self):
# Insertion of 'A' at position 1.
data = "T[-/A]GACACGTACGT"
parser = SnpSequence(data)
snps = parser.snps()
expected = [Snp('.1insA')]
self.assertEqual(snps, expected)
def test_Two_Substitutions(self):
# Substitution at position 5 and 6.
data = "TGACA[C/G][G/A]TACGT"
parser = SnpSequence(data)
snps = parser.snps()
expected = [Snp('.5C>G'), Snp('.6G>A')]
self.assertEqual(snps, expected)
def test_Substitution(self):
# Substitution at position 5.
data = "TGACA[C/G]GTACGT"
parser = SnpSequence(data)
snps = parser.snps()
expected = [Snp('.5C>G')]
self.assertEqual(snps, expected)
def test_Two_Deletions(self):
# Two deletions at positions 0 and 6.
data = "[T/-]GACAC[G/-]TACGT"
parser = SnpSequence(data)
snps = parser.snps()
expected = [Snp('.0del'), Snp('.6del')]
expected[0].ref_nucleotide = 'T'
expected[1].ref_nucleotide = 'G'
self.assertEqual(snps, expected)
def test_Two_Insertions(self):
# Allele1: TGACACGTACGT
# Insertion of 'A' at position 1 and
# Insertion of 'G' at position 6.
data = "T[-/A]GACA[-/G]CGTACGT"
parser = SnpSequence(data)
snps = parser.snps()
expected = [Snp('.1insA'), Snp('.6insG')]
self.assertEqual(snps, expected)
def test_SnpSameCharacter(self):
# Raise Starp Error if Snps have the same character.
data = "TGAC[A/A]CGTACGT"
with self.assertRaises(StarpError):
SnpSequence(data)
def test_InvalidChars(self):
# Raise Starp Error if there are bad characters.
data = "TGAC999ACGTACGT"
with self.assertRaises(StarpError):
SnpSequence(data)
def test_SyntaxError(self):
# Raise Starp Error if a bad string is entered.
data = "TGAC[ACGTACGT"
with self.assertRaises(StarpError):
SnpSequence(data)
def test_NoSnps(self):
data = "TGACACGTACGT"
parser = SnpSequence(data)
snps = parser.snps()
self.assertEqual(len(snps), 0)