def test_randomly_selects_correct_amount_of_items(self, mpopen, mpool):
mpopen.return_value.poll.return_value = None
mpopen.return_value.stdout.__iter__.return_value = self.samview_lines[1:]
mpopen.return_value.stdout.readline.return_value = self.samview_lines[0]
mpool.return_value.map = map
with mock.patch('subsamplebam.sys') as msys:
r = subsamplebam.subselect_from_bam(
'foo.bam', 10, 'chr1:1-10',
)
self.assertEqual(set(self.samview_lines), r)
def test_handles_missing_depth_error(self, mpopen, mpool):
mpopen.return_value.poll.return_value = None
mpopen.return_value.stdout.__iter__.return_value = self.samview_lines[1:]
mpopen.return_value.stdout.readline.return_value = self.samview_lines[0]
mpool.return_value.map = map
with mock.patch('subsamplebam.sys') as msys:
r = subsamplebam.subselect_from_bam(
'foo.bam', 11, 'chr1:1-10',
)
self.assertEqual(set([]), r)
for i in range(1,11):
msys.stderr.write.assert_has_call('Depth for chr1:{0}-{0} is only 10\n'.format(i))
def test_randomly_selects_correct_amount_of_items(self, mpopen, mpool):
mpopen.return_value.poll.return_value = None
mpopen.return_value.stdout.__iter__.return_value = self.samview_lines[
1:]
mpopen.return_value.stdout.readline.return_value = self.samview_lines[
0]
mpool.return_value.map = map
with mock.patch('subsamplebam.sys') as msys:
r = subsamplebam.subselect_from_bam(
'foo.bam',
10,
'chr1:1-10',
)
self.assertEqual(set(self.samview_lines), r)
def test_handles_missing_depth_error(self, mpopen, mpool):
mpopen.return_value.poll.return_value = None
mpopen.return_value.stdout.__iter__.return_value = self.samview_lines[
1:]
mpopen.return_value.stdout.readline.return_value = self.samview_lines[
0]
mpool.return_value.map = map
with mock.patch('subsamplebam.sys') as msys:
r = subsamplebam.subselect_from_bam(
'foo.bam',
11,
'chr1:1-10',
)
self.assertEqual(set([]), r)
for i in range(1, 11):
msys.stderr.write.assert_has_call(
'Depth for chr1:{0}-{0} is only 10\n'.format(i))
