def test_bad_bamfile_path_raises_exception(self):
self.module.subprocess = mock.Mock()
p = Params()
p.add(gtf='/path/to/GTF/mock.gtf')
p.add(feature_counts='/path/to/bin/featureCounts')
p.add(feature_counts_file_extension='counts')
p.add(feature_counts_output_dir='/path/to/final/featureCounts')
p.add(paired_alignment=False)
s1 = Sample('A', 'X')
s1.bamfiles = [
'/path/to/bamdir/A.bam', '/path/to/bamdir/A.primary.bam',
'/path/to/bamdir/A.primary.dedup.bam'
]
s2 = Sample('B', 'X')
s2.bamfiles = ['/path/to/bamdir/B.bam', '/bad/path/B.sort.bam']
project = Project()
project.add_parameters(p)
project.add_samples([s1, s2])
m = mock.MagicMock(side_effect=[True, True, True, True, False])
path = self.module.os.path
with mock.patch.object(path, 'isfile', m):
with self.assertRaises(self.module.MissingBamFileException):
self.module.execute_counting(project, util_methods)
def test_system_calls_single_end_experiment(self):
self.module.subprocess = mock.Mock()
p = Params()
p.add(gtf='/path/to/GTF/mock.gtf')
p.add(feature_counts='/path/to/bin/featureCounts')
p.add(feature_counts_file_extension='counts')
p.add(feature_counts_output_dir='/path/to/final/featureCounts')
p.add(paired_alignment=False)
s1 = Sample('A', 'X')
s1.bamfiles = [
'/path/to/bamdir/A.bam', '/path/to/bamdir/A.primary.bam',
'/path/to/bamdir/A.primary.dedup.bam'
]
project = Project()
project.add_parameters(p)
project.add_samples([s1])
m = mock.MagicMock(side_effect=[True, True, True])
path = self.module.os.path
with mock.patch.object(path, 'isfile', m):
self.module.execute_counting(project, util_methods)
calls = [
mock.call(
'/path/to/bin/featureCounts -a /path/to/GTF/mock.gtf -t exon -g gene_name -o /path/to/final/featureCounts/A.counts /path/to/bamdir/A.bam',
shell=True),
mock.call(
'/path/to/bin/featureCounts -a /path/to/GTF/mock.gtf -t exon -g gene_name -o /path/to/final/featureCounts/A.primary.counts /path/to/bamdir/A.primary.bam',
shell=True),
mock.call(
'/path/to/bin/featureCounts -a /path/to/GTF/mock.gtf -t exon -g gene_name -o /path/to/final/featureCounts/A.primary.dedup.counts /path/to/bamdir/A.primary.dedup.bam',
shell=True)
]
self.module.subprocess.check_call.assert_has_calls(calls)
# check that the sample contains paths to the new count files in the correct locations:
expected_files = [
os.path.join('/path/to/final/featureCounts',
re.sub('bam', 'counts', os.path.basename(f)))
for f in s1.bamfiles
]
actual_files = s1.countfiles
self.assertEqual(actual_files, expected_files)
def test_system_calls_paired_experiment(self):
mock_process = mock.Mock(name='mock_process')
mock_process.communicate.return_value = (('', ''))
mock_process.returncode = 0
mock_popen = mock.Mock(name='mock_popen')
mock_popen.return_value = mock_process
self.module.subprocess = mock.Mock()
self.module.subprocess.Popen = mock_popen
self.module.subprocess.STDOUT = ''
self.module.subprocess.PIPE = ''
p = Params()
cp = Params()
p.add(gtf='/path/to/GTF/mock.gtf')
cp.add(feature_counts='/path/to/bin/featureCounts')
cp.add(feature_counts_file_extension='counts')
cp.add(feature_counts_output_dir='/path/to/final/featureCounts')
p.add(paired_alignment=True)
s1 = Sample('A', 'X')
s1.bamfiles = [
'/path/to/bamdir/A.bam', '/path/to/bamdir/A.primary.bam',
'/path/to/bamdir/A.primary.dedup.bam'
]
project = Project()
project.add_parameters(p)
project.add_samples([s1])
m = mock.MagicMock(side_effect=[True, True, True])
path = self.module.os.path
with mock.patch.object(path, 'isfile', m):
self.module.execute_counting(project, cp, util_methods)
calls = [
mock.call(
'/path/to/bin/featureCounts -a /path/to/GTF/mock.gtf -t exon -g gene_name -p -o /path/to/final/featureCounts/A.counts /path/to/bamdir/A.bam',
shell=True,
stderr=self.module.subprocess.STDOUT,
stdout=self.module.subprocess.PIPE),
mock.call(
'/path/to/bin/featureCounts -a /path/to/GTF/mock.gtf -t exon -g gene_name -p -o /path/to/final/featureCounts/A.primary.counts /path/to/bamdir/A.primary.bam',
shell=True,
stderr=self.module.subprocess.STDOUT,
stdout=self.module.subprocess.PIPE),
mock.call(
'/path/to/bin/featureCounts -a /path/to/GTF/mock.gtf -t exon -g gene_name -p -o /path/to/final/featureCounts/A.primary.dedup.counts /path/to/bamdir/A.primary.dedup.bam',
shell=True,
stderr=self.module.subprocess.STDOUT,
stdout=self.module.subprocess.PIPE)
]
mock_popen.assert_has_calls(calls)
# check that the sample contains paths to the new count files in the correct locations:
expected_files = [
os.path.join('/path/to/final/featureCounts',
re.sub('bam', 'counts', os.path.basename(f)))
for f in s1.bamfiles
]
actual_files = s1.countfiles
self.assertEqual(actual_files, expected_files)