def test_bowtie_samples(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
b.bowtie_sample = MagicMock()
b.bowtie_samples(samples)
b.bowtie_sample.assert_any_call('POLR2A', None, '', ())
b.bowtie_sample.assert_any_call('ASDURF', None, '', ())
b.bowtie_sample.assert_any_call('POLR1C', None, '', ())
def test_run_bowtie_singlethread(testdir, mock_testclass):
sample = 'PORL2A'
bam = sample + '.bam'
fastq = sample + '_1.fastq'
copyfile(Path(__file__).parent.joinpath('samples.txt'), fastq)
fastq2 = sample + '_2.fastq'
copyfile(Path(__file__).parent.joinpath('samples.txt'), fastq2)
threads = 1
bowtie_args = (
'-x',
'sacCer3.fa',
)
subprocess.run = MagicMock(side_effect=create_file)
b.run_bowtie(fastq, fastq2, bam, threads, bowtie_args)
call1 = [
'bowtie2', '-x', 'sacCer3.fa', '-S', ANY, '-1', fastq, '-2', fastq2
]
call2 = ['samtools', 'view', '-b', '-o', ANY, ANY]
call3 = ['samtools', 'sort', '-o', bam, ANY]
subprocess.run.assert_any_call(call1, check=True)
subprocess.run.assert_any_call(call2, check=True)
subprocess.run.assert_any_call(call3, check=True)
subprocess.run.assert_has_calls([
call(call1, check=True),
call(call2, check=True),
call(call3, check=True)
], True)
assert subprocess.run.call_args_list[0].args[0][
4] == subprocess.run.call_args_list[1].args[0][5]
assert subprocess.run.call_args_list[1].args[0][
4] == subprocess.run.call_args_list[2].args[0][4]
def test_bowtie_sample_single(testdir, mock_testclass):
sample = 'PORL2A'
bam = sample + '.bam'
fastq = sample + '_1.fastq'
b.run_bowtie = MagicMock()
Fastq.fastq = MagicMock(side_effect=[fastq, None])
b.bowtie_sample(sample)
Fastq.fastq.assert_any_call(sample, 1)
Fastq.fastq.assert_any_call(sample, 2)
b.run_bowtie.assert_called_once_with(fastq, None, bam, None, ())
def test_bowtie_samples_parameters(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
threads = 2
output_suffix = '-sacCer'
bowtie_args = (
'-x',
'sacCer3.fa',
)
b.bowtie_sample = MagicMock()
b.bowtie_samples(samples, threads, output_suffix, bowtie_args=bowtie_args)
b.bowtie_sample.assert_any_call('POLR2A', threads, output_suffix,
bowtie_args)
b.bowtie_sample.assert_any_call('ASDURF', threads, output_suffix,
bowtie_args)
b.bowtie_sample.assert_any_call('POLR1C', threads, output_suffix,
bowtie_args)
def test_bowtie_sample_parameters(testdir, mock_testclass):
sample = 'PORL2A'
output_suffix = '-sacCer'
bam = sample + output_suffix + '.bam'
fastq = sample + '_1.fastq'
fastq2 = sample + '_2.fastq'
threads = 2
bowtie_args = (
'-x',
'sacCer3.fa',
)
b.run_bowtie = MagicMock()
Fastq.fastq = MagicMock(side_effect=[fastq, fastq2])
b.bowtie_sample(sample, threads, output_suffix, bowtie_args=bowtie_args)
Fastq.fastq.assert_any_call(sample, 1)
Fastq.fastq.assert_any_call(sample, 2)
b.run_bowtie.assert_called_once_with(fastq, fastq2, bam, threads,
bowtie_args)
def test_run_bowtie_fastq2notexists(testdir, mock_testclass):
sample = 'PORL2A'
bam = sample + '.bam'
fastq = sample + '_1.fastq'
copyfile(Path(__file__).parent.joinpath('samples.txt'), fastq)
fastq2 = sample + '_2.fastq'
subprocess.run = MagicMock(side_effect=create_file)
b.run_bowtie(fastq, None, bam, None, ())
call1 = ['bowtie2', '-S', ANY, '-U', fastq]
call2 = ['samtools', 'view', '-b', '-o', ANY, ANY]
call3 = ['samtools', 'sort', '-o', bam, ANY]
subprocess.run.assert_any_call(call1, check=True)
subprocess.run.assert_any_call(call2, check=True)
subprocess.run.assert_any_call(call3, check=True)
subprocess.run.assert_has_calls([
call(call1, check=True),
call(call2, check=True),
call(call3, check=True)
], True)
assert subprocess.run.call_args_list[0].args[0][
2] == subprocess.run.call_args_list[1].args[0][5]
assert subprocess.run.call_args_list[1].args[0][
4] == subprocess.run.call_args_list[2].args[0][4]
def test_bowtie_samples_second(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
b.bowtie_sample = MagicMock()
b.bowtie_samples(samples, index=1)
b.bowtie_sample.assert_called_once_with('ASDURF', None, '', ())