def test_indels(self):
''' Indel handling '''
row = [
'thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD',
'0/1:5,10,1'
]
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['GA']))
row = [
'thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD',
'0/1:5,5,2'
]
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['G', 'GA']))
row = [
'thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD',
'0/1:5,5,3'
]
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['G', 'GA', 'T']))
row = [
'thecontig', '105000', '.', 'AT', 'A', '.', '.', '.', 'GT:AD',
'0/1:2,10'
]
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1']))
self.assertEqual(out, [('thecontig', 105000, 105001, 's1', ['A'])])
def test_dp_inaccurate(self):
''' The DP might not equal the sum of the ADs and that's okay apparently. '''
row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:5:2,2']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(set(out[0][4]), set(['G', 'A']))
row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:2:3,3']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['G', 'A']))
row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:10:2,0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out, [])
def test_dp_inaccurate(self):
''' The DP might not equal the sum of the ADs and that's okay apparently. '''
row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:5:2,2']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(set(out[0][4]), set(['G', 'A']))
row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:2:3,3']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['G', 'A']))
row = ['chr10', '105', '.', 'G', 'A', '.', '.', '.', 'GT:DP:AD', '0/1/1:10:2,0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out, [])
def test_indels(self):
''' Indel handling '''
row = ['thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD', '0/1:5,10,1']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['GA']))
row = ['thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD', '0/1:5,5,2']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['G', 'GA']))
row = ['thecontig', '105000', '.', 'G', 'GA,T', '.', '.', '.', 'GT:AD', '0/1:5,5,3']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['G', 'GA', 'T']))
row = ['thecontig', '105000', '.', 'AT', 'A', '.', '.', '.', 'GT:AD', '0/1:2,10']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1']))
self.assertEqual(out, [('thecontig', 105000, 105001, 's1', ['A'])])
def test_invariant_sites(self):
''' Invariant site handling is slightly different in code, so test it specially. '''
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT:DP', '0/0:3']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', '0/0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=0))
self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', '0/0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(out, [])
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', './.']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(out, [])
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT:DP', './.:10']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])
def test_invariant_sites(self):
''' Invariant site handling is slightly different in code, so test it specially. '''
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT:DP', '0/0:3']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', '0/0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=0))
self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', '0/0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(out, [])
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT', './.']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(out, [])
row = ['LASV.l', '1', '.', 'T', '.', '.', '.', '.', 'GT:DP', './.:10']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(out, [('LASV.l', 1, 1, 's1', ['T'])])
def test_het_edgecases(self):
''' The interplay between min_coverage and major_cutoff is not obvious, here's
what I understand from Kristian about the desired behavior.
for min_dp=3:
3G, 4A, 5C -> G/A/C
2G, 3A, 3T -> A/T
2A, 2T -> no call
2G, 3C -> C
2A, 3C, 4T -> T
for min_dp=2:
2A, 2T -> A/T
'''
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:3,4,5,0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['G', 'A', 'C']))
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:2,3,0,3']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['A', 'T']))
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,0,2']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out, [])
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,0,2']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=2))
self.assertEqual(set(out[0][4]), set(['A', 'T']))
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:2,0,3,0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out[0][4], ['C'])
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,3,4']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out[0][4], ['T'])
def test_het_edgecases(self):
''' The interplay between min_coverage and major_cutoff is not obvious, here's
what I understand from Kristian about the desired behavior.
for min_dp=3:
3G, 4A, 5C -> G/A/C
2G, 3A, 3T -> A/T
2A, 2T -> no call
2G, 3C -> C
2A, 3C, 4T -> T
for min_dp=2:
2A, 2T -> A/T
'''
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:3,4,5,0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['G', 'A', 'C']))
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:2,3,0,3']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(set(out[0][4]), set(['A', 'T']))
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,0,2']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out, [])
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,0,2']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=2))
self.assertEqual(set(out[0][4]), set(['A', 'T']))
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:2,0,3,0']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out[0][4], ['C'])
row = ['thecontig', '105000', '.', 'G', 'A,C,T', '.', '.', '.', 'GT:AD', '0/1:0,2,3,4']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=3))
self.assertEqual(out[0][4], ['T'])
def test_missing_dp(self):
''' VCF files might contain rows with no calls or any kind of data and that's okay. '''
row = ['chr10', '105', '.', 'G', '.', '.', '.', '.', 'GT', './.']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(out, [])
def test_missing_dp(self):
''' VCF files might contain rows with no calls or any kind of data and that's okay. '''
row = ['chr10', '105', '.', 'G', '.', '.', '.', '.', 'GT', './.']
out = list(assembly.vcfrow_parse_and_call_snps(row, ['s1'], min_dp=1))
self.assertEqual(out, [])
