def get_raw_reads(bamfile, regionstr=""):
'''
:param str bamfile: path to input file
:param str regionstr: the seq id to select, followed by the region to look up, seperated by colon. i.e.:
<refid>:1-1000
:return a list of sequences from the output of `samtools view`
'''
return list(subsamplebam.samview(bamfile, regionstr))
def get_raw_reads(bamfile, regionstr=""): ''' :param str bamfile: path to input file :param str regionstr: the seq id to select, followed by the region to look up, seperated by colon. i.e.: <refid>:1-1000 :return a list of sequences from the output of `samtools view` ''' return list(subsamplebam.samview(bamfile, regionstr))
def test_samtools_returns_non0_raises_valueerror(self, mpopen, msys):
mock_popen = mock.MagicMock()
mock_popen.poll.return_value = 1
mock_popen.stdout.readline.return_value = ''
mock_popen.stdout.__iter__.return_value = []
mpopen.return_value = mock_popen
r = subsamplebam.samview('foo.bam', 'chr1:1-100')
self.assertRaises(ValueError, next, r)
def test_samtools_returns_non0_raises_valueerror(self, mpopen, msys):
mock_popen = mock.MagicMock()
mock_popen.poll.return_value = 1
mock_popen.stdout.readline.return_value = ''
mock_popen.stdout.__iter__.return_value = []
mpopen.return_value = mock_popen
r = subsamplebam.samview('foo.bam', 'chr1:1-100')
self.assertRaises(ValueError, next, r)
def test_0_line_samtools_view_no_error(self, mpopen, msys):
mock_popen = mock.MagicMock()
mock_popen.poll.return_value = 0
mock_popen.stdout.readline.return_value = ''
mock_popen.stdout.__iter__.return_value = []
mpopen.return_value = mock_popen
r = subsamplebam.samview('foo.bam', 'chr1:1-100')
lines = list(r)
self.assertEqual([''], lines)
def test_0_line_samtools_view_no_error(self, mpopen, msys):
mock_popen = mock.MagicMock()
mock_popen.poll.return_value = 0
mock_popen.stdout.readline.return_value = ''
mock_popen.stdout.__iter__.return_value = []
mpopen.return_value = mock_popen
r = subsamplebam.samview('foo.bam', 'chr1:1-100')
lines = list(r)
self.assertEqual([''], lines)
def test_returns_samtools_view_output_as_subprocess_stdout(self, mpopen, msys):
samlines = ['line1', 'line2', 'line3']
mock_popen = mock.MagicMock()
mock_popen.poll.return_value = None
mock_popen.stdout.readline.return_value = samlines[0]
mock_popen.stdout.__iter__.return_value = samlines[1:]
mpopen.return_value = mock_popen
r = subsamplebam.samview('foo.bam', 'chr1:1-100')
cmd = 'samtools view foo.bam chr1:1-100'
for eline, rline in zip(samlines, r):
self.assertEqual(eline, rline)
mpopen.assert_called_once_with(cmd.split(), stdout=-1)
msys.stderr.write.assert_called_with(cmd + '\n')
def test_returns_samtools_view_output_as_subprocess_stdout(
self, mpopen, msys):
samlines = ['line1', 'line2', 'line3']
mock_popen = mock.MagicMock()
mock_popen.poll.return_value = None
mock_popen.stdout.readline.return_value = samlines[0]
mock_popen.stdout.__iter__.return_value = samlines[1:]
mpopen.return_value = mock_popen
r = subsamplebam.samview('foo.bam', 'chr1:1-100')
cmd = 'samtools view foo.bam chr1:1-100'
for eline, rline in zip(samlines, r):
self.assertEqual(eline, rline)
mpopen.assert_called_once_with(cmd.split(), stdout=-1)
msys.stderr.write.assert_called_with(cmd + '\n')
