def test_fetch(self):
''' can fetch variants within a genomic region
'''
chrom, start, stop = '01', 5000, 50000
bfile = BgenFile(self.folder / 'example.16bits.bgen')
self.assertTrue(
bfile._check_for_index(str(self.folder / 'example.16bits.bgen')))
self.assertTrue(list(bfile.fetch('02')) == [])
def test_fetch_in_region(self):
''' fetching variants with chrom, start, stop gives variants in region
'''
chrom, start, stop = '01', 5000, 50000
bfile = BgenFile(self.folder / 'example.16bits.bgen')
sortkey = lambda x: (x.chrom, x.pos)
gen_vars = [
x for x in sorted(self.gen_data, key=sortkey)
if start <= x.pos <= stop
]
for x, y in zip(sorted(bfile.fetch(chrom, start, stop), key=sortkey),
gen_vars):
self.assertEqual(x.rsid, y.rsid)
self.assertEqual(x.chrom, y.chrom)
self.assertEqual(x.pos, y.pos)
# check that we don't get any variants in a region without any
self.assertEqual(list(bfile.fetch(chrom, start * 1000, stop * 1000)),
[])
def test_fetch_whole_chrom(self):
''' fetching just with chrom gives all variants on chromosome
'''
chrom, start, stop = '01', 5000, 50000
bfile = BgenFile(self.folder / 'example.16bits.bgen')
# test fetching a whole chromosome
sortkey = lambda x: (x.chrom, x.pos)
for x, y in zip(sorted(bfile.fetch(chrom), key=sortkey),
sorted(self.gen_data, key=sortkey)):
self.assertEqual(x.rsid, y.rsid)
self.assertEqual(x.chrom, y.chrom)
self.assertEqual(x.pos, y.pos)
def test_fetch_after_position(self):
''' fetching variants with chrom and start gives all variants after pos
'''
chrom, start, stop = '01', 5000, 50000
bfile = BgenFile(self.folder / 'example.16bits.bgen')
sortkey = lambda x: (x.chrom, x.pos)
gen_vars = [
x for x in sorted(self.gen_data, key=sortkey) if start <= x.pos
]
for x, y in zip(sorted(bfile.fetch(chrom, start), key=sortkey),
gen_vars):
self.assertEqual(x.rsid, y.rsid)
self.assertEqual(x.chrom, y.chrom)
self.assertEqual(x.pos, y.pos)