def test_tarball_fail_missing_data(self):
inDir = util.file.get_test_input_path(self)
with illumina.IlluminaDirectory(
os.path.join(inDir, 'bcl-runinfo.tar.gz')) as idir:
self.assertRaises(Exception, idir.get_SampleSheet())
with illumina.IlluminaDirectory(
os.path.join(inDir, 'bcl-samplesheet.tar.gz')) as idir:
self.assertRaises(Exception, idir.get_RunInfo())
def test_tarball_normal(self):
inDir = util.file.get_test_input_path(self)
with illumina.IlluminaDirectory(os.path.join(inDir,
'bcl-plain.tgz')) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))
with illumina.IlluminaDirectory(
os.path.join(inDir, 'bcl-plain.tar.bz2')) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))
def test_tarball_sample_sheet(self):
inDir = util.file.get_test_input_path(self)
with illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-samplesheet.tar.gz')) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))
self.assertEqual(len(idir.get_SampleSheet().get_rows()), 15)
with illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-both.tar.gz')) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))
self.assertEqual(len(idir.get_SampleSheet().get_rows()), 15)
def test_tarball_run_info(self):
inDir = util.file.get_test_input_path(self)
with illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-runinfo.tar.gz')) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))
self.assertEqual(idir.get_RunInfo().get_flowcell(), 'AHVPA')
self.assertEqual(idir.get_RunInfo().get_machine(), 'M04004')
self.assertEqual(idir.get_RunInfo().get_rundate_iso(), '2015-08-27')
with illumina.IlluminaDirectory(os.path.join(inDir, 'bcl-both.tar.gz')) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))
self.assertEqual(idir.get_RunInfo().get_flowcell(), 'AHVPA')
self.assertEqual(idir.get_RunInfo().get_read_structure(), '101T8B8B101T')
def test_directory(self):
inDir = util.file.get_test_input_path(self)
test_in = os.path.join(inDir, 'empty_dir')
with illumina.IlluminaDirectory(test_in) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))
def test_zip_archive(self):
inDir = util.file.get_test_input_path(self)
with illumina.IlluminaDirectory(os.path.join(
inDir, 'bcl-both-2.zip')) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))
self.assertEqual(len(idir.get_SampleSheet().get_rows()), 15)
def test_tarball_indented(self):
inDir = util.file.get_test_input_path(self)
with illumina.IlluminaDirectory(os.path.join(
inDir, 'bcl-indented.tgz')) as idir:
self.assertTrue(os.path.isdir(idir.get_BCLdir()))