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_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_del_and_ins(self):
# Deletion at position 0 and insertion of 'T' at position 4.
data = ">Allele1\nTGAC-ACGTACGT\n>Allele2\n-GACTACGTACGT"
parser = TwoAlleles(data)
snps = parser.snps()
expected = [Snp('.0del'), Snp('.4insT')]
expected[0].ref_nucleotide = 'T'
self.assertEqual(snps, expected)
def test_Two_Insertions(self):
# Allele1 = TGACACGTACGT
# Insertion of 'A' at position 1 and 'G' at position 8.
data = ">Allele1\nT-GACACG-TACGT\n>Allele2\nTAGACACGGTACGT"
parser = TwoAlleles(data)
snps = parser.snps()
expected = [Snp('.1insA'), Snp('.8insG')]
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_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_Deletions(self):
# Two deletions at positions 9 and 11.
data = ">Allele1\nTGACACGTACGT\n>Allele2\nTGACACGTA-G-"
parser = TwoAlleles(data)
snps = parser.snps()
expected = [Snp('.9del'), Snp('.11del')]
expected[0].ref_nucleotide = 'C'
expected[1].ref_nucleotide = 'T'
self.assertEqual(snps, expected)
def test_rev_comp(self):
data = """>H26A region
TGCGATGACGGAAAAAAAAAGGTGGTGGGAGTATGACGAAAATAAACCAGCGAAAATTAACCGCGCGGACTATTCATCAAGTCGTCCATTAGGAGTAGAGATTTTCACAACCCAATTTGCCTATTTTATTTA
>H26A region
TGCGATGACGGAAAAAAAAAGGTGGTGGGAGTATGACGA-AATAAACCAGCGAAAATTAACCGCGCGGACTATTCATCAAGTCGTCCATTAGGAGTAGAGATTTTCACAACCCAATTTGCCTATTTTATTTA"""
parser = TwoAlleles(data)
snp = parser.snps()[0]
expected = Snp(descriptor='.39del')
expected.ref_nucleotide = 'A'
self.assertEqual(expected, snp)
def test_single_blast_parser(self):
sequence = """
Query 1 TGCGATGACGGAAAAAAAAAGGTGGTGGGAGTATGACGAAAATAAACCAGCGAAAATTAA 60
|||||||| ||||||||||||| |||||||||||||||||||||||||||||||||||||
Sbjct 528388742 TGCGATGA-GGAAAAAAAAAGGCGGTGGGAGTATGACGAAAATAAACCAGCGAAAATTAA 528388684
Query 61 CCG-GCGGACTATTCACCAAGTCGTCCATTAGGAGTAGAGAT 102
||| ||||||||||||||||||||||||||||||||||||||
Sbjct 528388683 CCGTGCGGACTATTCACCAAGTCGTCCATTAGGAGTAGAGAT 528388642"""
parser = SingleBlastParser(sequence)
snps = parser.snps()
expected = [Snp('.8del'), Snp('.22T>C'), Snp('.63insT')]
expected[0].ref_nucleotide = 'C'
self.assertEqual(expected, snps)
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_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_Substitution(self):
# Substitution at position 6: G>C
data = ">Allele1\nTGACACGTACGT\n>Allele2\nTGACACCTACGT"
parser = TwoAlleles(data)
snps = parser.snps()
expected = [Snp('.6G>C')]
self.assertEqual(snps, expected)
def test_init_one_deletion(self):
descriptor = 'NG_012232.1:g.19del'
snp = Snp(descriptor)
self.assertEqual(snp.prefix, 'NG_012232.1:g.')
self.assertEqual(snp.position, 19)
self.assertEqual(snp.type, 'deletion')
self.assertEqual(snp.ref_nucleotide, '')
self.assertEqual(snp.new_nucleotide, '')
def test_init_one_insertion(self):
descriptor = 'NC_000023.10:g.32867861insT'
snp = Snp(descriptor)
self.assertEqual(snp.prefix, 'NC_000023.10:g.')
self.assertEqual(snp.position, 32867861)
self.assertEqual(snp.type, 'insertion')
self.assertEqual(snp.ref_nucleotide, '')
self.assertEqual(snp.new_nucleotide, 'T')
def test_init_one_subsitution(self):
descriptor = 'NC_000023.10:g.33038255C>A'
snp = Snp(descriptor)
self.assertEqual(snp.prefix, 'NC_000023.10:g.')
self.assertEqual(snp.position, 33038255)
self.assertEqual(snp.type, 'substitution')
self.assertEqual(snp.ref_nucleotide, 'C')
self.assertEqual(snp.new_nucleotide, 'A')
def test_One_Deletion(self):
# Deletion at position 9.
data = ">Allele1\nTGACACGTACGT\n>Allele2\nTGACACGTA-GT"
parser = TwoAlleles(data)
snps = parser.snps()
expected = [Snp('.9del')]
expected[0].ref_nucleotide = 'C'
self.assertEqual(snps, expected)
def test_simple_prefix(self):
descriptor = '.12C>G'
snp = Snp(descriptor)
self.assertEqual(snp.prefix, '.')
def test_One_Insertion(self):
data = ">Allele1\nT-GACACGTACGT\n>Allele2\nTAGACACGTACGT"
parser = TwoAlleles(data)
snps = parser.snps()
expected = [Snp('.1insA')]
self.assertEqual(snps, expected)
