def header(self, handle):
self._header = Header()
for line in handle:
try:
self._header.append(line)
except ValueError:
break
self.first = line
# make sure all the header data is available within variants
Variant.set_header(self._header)
def test_variant_with_samples(self):
''' check that we can construct a Variant with sample data
'''
line = '1\t100\t.\tA\tG\t.\t.\tAD=100\tGT:PL\t1/1:80,9,2\n'
var = Variant(line)
self.assertIsInstance(var.samples, Samples)
self.assertEqual(str(var), line)
# check it works for variants with multiple samples
line = '1\t100\t.\tA\tG\t.\t.\tAC=9\tGT:PL\t1/1:80,9,2\t0/1:9,1,1\n'
var = Variant(line)
self.assertEqual(str(var), line)
def test_variant_alts(self):
''' check we can set a variant alt alleles
'''
line = '1\t100\t.\tA\tG\t.\t.\tAC=100\n'
var = Variant(line)
var.alts = 'G,C'
self.assertEqual(var.alts, ['G', 'C'])
var.alts = ['G', 'T']
self.assertEqual(var.alts, ['G', 'T'])
var.alts = 'G'
self.assertEqual(var.alts, ['G'])
def test_variant_multiallelic(self):
''' check initialising a multiallelic Variant
'''
line = '1\t100\t.\tA\tG,C\t.\t.\tAC=100\n'
var = Variant(line)
self.assertEqual(var.alts, ['G', 'C'])
def test_remap_missing_alt(self):
''' check remapping a variant without alts
'''
genome = None
var = Variant('1\t1000000\t.\tA\t.\t100\tPASS\tAC=100\n')
var = remap(self.lift, var, genome)
self.assertEqual(var.chrom, '1')
self.assertEqual(var.pos, 1064620)
def test_variant_init(self):
''' check initialising a Variant
'''
line = '1\t100\t.\tA\tG\t.\t.\tAC=100\n'
var = Variant(line)
self.assertEqual(var.chrom, '1')
self.assertEqual(var.pos, 100)
self.assertEqual(var.ref, 'A')
self.assertEqual(var.ref, 'A')
self.assertEqual(var.alts, ['G'])
self.assertIsInstance(var.info, Info)
self.assertEqual(var.info, Info('AC=100'))
self.assertIsNone(var.samples)
self.assertEqual(str(var), line)
def test_remap_unknown_chrom(self):
''' check a variant where the variant maps to a non-standard chromosome
'''
genome = None
var = Variant('1\t13027995\t.\tA\tG\t100\tPASS\tAC=100\n')
self.assertIsNone(remap(self.lift, var, genome))
def test_remap_not_in_build(self):
''' check a variant where the position is not in the new build
'''
genome = None
var = Variant('1\t1\t.\tA\tG\t100\tPASS\tAC=100\n')
self.assertIsNone(remap(self.lift, var, genome))
def __next__(self):
if self.first is not None:
line, self.first = self.first, None # get value and blank self.first
return Variant(line)
return Variant(next(self.handle))