def test_parse_samplesheet(self):
"""Write and parse a csv-file
"""
# Assert non-existing file raises exception
with self.assertRaises(IOError):
HiSeqRun.parse_samplesheet(os.path.join(self.rootdir,'non-existing-samplesheet'))
# Write a csv file with some bogus values
sdata = td.generate_samplesheet_data()
samplesheet = os.path.join(self.rootdir,'SampleSheet.csv')
HiSeqRun.write_samplesheet(sdata,samplesheet)
# Assert that the written data corresponds to the generated data
with open(samplesheet) as fh:
# Assert that header is correct
self.assertListEqual(HiSeqRun._samplesheet_header(),
fh.next().strip().split(","),
"Written header does not match expected header")
for entry in sdata:
# Assert that all rows have the correct values in the correct columns
self.assertListEqual([str(e) for e in entry],
fh.next().strip().split(","),
"Written data row does not match entry in generated samplesheet")
# Assert that all rows from samplesheet has been consumed
with self.assertRaises(StopIteration):
fh.next()
# Assert that the parsed data matches the generated data
data = HiSeqRun.parse_samplesheet(samplesheet)
self.assertEqual(len(sdata),
len(data),
"Number of parsed entries does not match number of generated entries")
for d in data:
self.assertListEqual([str(e) for e in sdata.pop(0)],
[d[col] for col in HiSeqRun._samplesheet_header()],
"Parsed data row does not match entry in generated samplesheet")
# Assert that filtering on lane returns expected output
lanes = list(set([d["Lane"] for d in data]))
obs_lane_data = HiSeqRun.parse_samplesheet(samplesheet,lane=lanes[-1])
exp_lane_data = [d for d in data if str(d["Lane"]) == str(lanes[-1])]
self.assertListEqual(sorted(obs_lane_data),
sorted(exp_lane_data),
"Parsed data row does not match entry in generated samplesheet")
