def setUp(self):
self.rootdir = tempfile.mkdtemp(prefix="test_illumina_run_")
# Create a fcdir
self.exp_fcid = td.generate_fc_barcode()
self.exp_fcdir = os.path.join(self.rootdir,td.generate_run_id(fc_barcode=self.exp_fcid))
os.mkdir(self.exp_fcdir)
# Create multiple sequence read directories
self.exp_seqdir = [os.path.join(self.exp_fcdir,"Unaligned"),
os.path.join(self.exp_fcdir,"Unaligned_L6"),
os.path.join(self.exp_fcdir,"Unaligned_L8")]
for d in self.exp_seqdir:
os.mkdir(d)
# Create directories for undetermined indices reads
self.exp_unmatched_directory = [os.path.join(d,"Undetermined_indices") for d in self.exp_seqdir[:-1]]
for d in self.exp_unmatched_directory:
os.mkdir(d)
# Create basecall stats directories
self.exp_basecall_stats = [os.path.join(d,"Basecall_Stats_{}".format(self.exp_fcid)) for d in self.exp_seqdir[1:]]
for d in self.exp_basecall_stats:
os.mkdir(d)
self.run = IlluminaRun(self.exp_fcdir)
def test_get_samplesheet(self):
"""Locate the samplesheet in a folder
"""
# Work in a separate subdirectory
subdir = os.path.join(self.rootdir,"test_get_samplesheet")
os.mkdir(subdir)
# Create a few random files and folders and assert that they are not returned
suffixes = [".csv","",""]
for n in range(3):
os.mkdir(os.path.join(subdir,''.join(random.choice(string.ascii_uppercase) for x in range(5))))
fh, _ = tempfile.mkstemp(dir=subdir, suffix=suffixes[n])
os.close(fh)
self.assertIsNone(IlluminaRun.get_samplesheet(subdir),
"Getting non-existing samplesheet did not return None")
# Create a SampleSheet.csv and a [FCID].csv file and assert that they are
# returned with a preference for the [FCID].csv file
fcid = td.generate_fc_barcode()
fcdir = os.path.join(subdir,td.generate_run_id(fc_barcode=fcid))
os.mkdir(fcdir)
ss = [os.path.join(fcdir,"SampleSheet.csv"),
os.path.join(fcdir,"{}.csv".format(fcid))]
for s in ss:
utils.touch_file(s)
self.assertEqual(s,IlluminaRun.get_samplesheet(fcdir),
"Did not get existing {}".format(os.path.basename(s)))
shutil.rmtree(subdir)
def test_get_samplesheet(self):
"""Test that the _get_samplesheet method behaves as expected
"""
# Create a few random files and folders and assert that they are not returned
suffixes = [".csv","",""]
for n in range(3):
os.mkdir(os.path.join(self.rootdir,''.join(random.choice(string.ascii_uppercase) for x in range(5))))
fh, _ = tempfile.mkstemp(dir=self.rootdir, suffix=suffixes[n])
os.close(fh)
self.assertIsNone(sq.get_samplesheet(self.rootdir),
"Getting non-existing samplesheet did not return None")
# Create a SampleSheet.csv and a [FCID].csv file and assert that they are
# returned with a preference for the [FCID].csv file
fcid = td.generate_fc_barcode()
fcdir = os.path.join(self.rootdir,td.generate_run_id(fc_barcode=fcid))
os.mkdir(fcdir)
ss = [os.path.join(fcdir,"SampleSheet.csv"),
os.path.join(fcdir,"{}.csv".format(fcid))]
for s in ss:
utils.touch_file(s)
self.assertEqual(s,sq.get_samplesheet(fcdir),
"Did not get existing {}".format(os.path.basename(s)))
def setUp(self):
self.rootdir = tempfile.mkdtemp(prefix="test_illumina_run_")
# Create a fcdir
self.exp_fcid = td.generate_fc_barcode()
self.exp_fcdir = os.path.join(
self.rootdir, td.generate_run_id(fc_barcode=self.exp_fcid))
os.mkdir(self.exp_fcdir)
# Create multiple sequence read directories
self.exp_seqdir = [
os.path.join(self.exp_fcdir, "Unaligned"),
os.path.join(self.exp_fcdir, "Unaligned_L6"),
os.path.join(self.exp_fcdir, "Unaligned_L8")
]
for d in self.exp_seqdir:
os.mkdir(d)
# Create directories for undetermined indices reads
self.exp_unmatched_directory = [
os.path.join(d, "Undetermined_indices")
for d in self.exp_seqdir[:-1]
]
for d in self.exp_unmatched_directory:
os.mkdir(d)
# Create basecall stats directories
self.exp_basecall_stats = [
os.path.join(d, "Basecall_Stats_{}".format(self.exp_fcid))
for d in self.exp_seqdir[1:]
]
for d in self.exp_basecall_stats:
os.mkdir(d)
self.run = IlluminaRun(self.exp_fcdir)
def test_get_flowcelldirs(self):
"""Test that the _get_flowcelldirs method behaves as expected
"""
# Create a few random files and folders and assert that they are not returned
for n in range(3):
os.mkdir(os.path.join(self.rootdir,''.join(random.choice(string.ascii_uppercase) for x in range(5))))
fh, _ = tempfile.mkstemp(dir=self.rootdir)
os.close(fh)
self.assertListEqual([], sq.get_flowcelldirs(self.rootdir),
"Listing available flowcells did not return an empty list")
# Create a few flowcell directories and make sure that they are returned
fcdirs = []
for n in range(3):
fcdirs.append(os.path.join(self.rootdir,td.generate_run_id()))
os.mkdir(fcdirs[-1])
fcdirs = sorted(fcdirs)
self.assertListEqual(fcdirs,sorted(sq.get_flowcelldirs(self.rootdir)),
"Listing available flowcells did not return the 3 expected folders")
# Test that filtering based on flowcell name works
self.assertListEqual([fcdirs[-1]],sq.get_flowcelldirs(self.rootdir,os.path.basename(fcdirs[-1])),
"Filtering based on flowcell name did not returned the expected output")
# Test that filtering based on partial flowcell name works
self.assertListEqual([fcdirs[-1]],sq.get_flowcelldirs(self.rootdir,os.path.basename(fcdirs[-1][10:])),
"Filtering based on partial flowcell name did not returned the expected output")
