def test_invalid_spreadsheet_doesnt_exist(self):
'''test_invalid_spreadsheet_doesnt_exist'''
i = SpreadsheetParser(os.path.join(data_dir,
'file_which_doesnt_exist'))
with self.assertRaises(Exception):
i.extract_samples()
def test_spreadsheet_with_one_set_of_files(self):
'''A spreadsheet with one set of files should give a single object back'''
i = SpreadsheetParser(
os.path.join(data_dir, 'spreadsheet_with_one_set_of_files.csv'))
samples = i.extract_samples()
self.assertEqual(len(samples), 1)
self.assertEqual(
samples[0].forward_file,
'plasmidtron/tests/data/spreadsheetparser/sampleA_1.fastq.gz')
self.assertEqual(
samples[0].reverse_file,
'plasmidtron/tests/data/spreadsheetparser/sampleA_2.fastq.gz')
def test_spreadsheet_with_a_non_paired_file(self):
'''A spreadsheet with a single file should be okay'''
i = SpreadsheetParser(
os.path.join(data_dir, 'spreadsheet_with_a_non_paired_file.csv'),
False)
samples = i.extract_samples()
self.assertEqual(len(samples), 1)
self.assertEqual(
samples[0].forward_file,
'plasmidtron/tests/data/spreadsheetparser/sampleA.fasta')
self.assertEqual(samples[0].basename, 'sampleA')