def test_cit_magic_fail_option4(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '4'
program_ran, error_message = cit_magic.convert(**options)
self.assertFalse(program_ran)
self.assertEqual(error_message, "naming convention option [4] must be in form 4-Z where Z is an integer")
def test_cit_magic_succeed_option4(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '4-3'
program_ran, outfile = cit_magic.convert(**options)
self.assertTrue(program_ran)
expected_file = os.path.join('measurements.txt')
self.assertEqual(outfile, expected_file)
def test_cit_magic_succeed_option4(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '4-3'
program_ran, outfile = cit_magic.convert(**options)
self.assertTrue(program_ran)
expected_file = os.path.join('measurements.txt')
self.assertEqual(outfile, expected_file)
def test_cit_magic_with_file(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
program_ran, outfile = cit_magic.convert(**options)
self.assertTrue(program_ran)
expected_file = os.path.join('measurements.txt')
self.assertEqual(outfile, expected_file)
meas_df = nb.MagicDataFrame(outfile)
self.assertIn('sequence', meas_df.df.columns)
def test_cit_magic_with_file(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
program_ran, outfile = cit_magic.convert(**options)
self.assertTrue(program_ran)
expected_file = os.path.join('measurements.txt')
self.assertEqual(outfile, expected_file)
meas_df = nb.MagicDataFrame(outfile)
self.assertIn('sequence', meas_df.df.columns)
def test_cit_magic_fail_option4(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '4'
program_ran, error_message = cit_magic.convert(**options)
self.assertFalse(program_ran)
self.assertEqual(
error_message,
"naming convention option [4] must be in form 4-Z where Z is an integer"
)
def test_cit_magic_with_other_data(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '1'
options['methods'] = ['SO-SM:SO-MAG']
options['locname'] = 'location'
options['avg'] = 1
options['specnum'] = 2
program_ran, outfile = cit_magic.convert(**options)
self.assertTrue(program_ran)
expected_file = os.path.join('measurements.txt')
self.assertEqual(outfile, expected_file)
def test_cit_magic_with_other_data(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '1'
options['methods'] = ['SO-SM:SO-MAG']
options['locname'] = 'location'
options['avg'] = 1
options['specnum'] = 2
program_ran, outfile = cit_magic.convert(**options)
self.assertTrue(program_ran)
expected_file = os.path.join('measurements.txt')
self.assertEqual(outfile, expected_file)
def test_cit_magic_with_path(self):
options = {}
#options['input_dir_path'] = os.path.join(WD, 'data_files',
# 'Measurement_Import',
# 'CIT_magic', 'PI47')pppp
options['magfile'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47', 'PI47-.sam')
options['loc_file'] = 'custom_locations.txt'
options['samp_file'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'CIT_magic', 'PI47', 'custom_samples.txt')
options['dir_path'] = os.path.join(WD, 'data_files')
program_ran, outfile = cit_magic.convert(**options)
self.assertTrue(program_ran)
expected_file = os.path.join('measurements.txt')
self.assertEqual(outfile, expected_file)
for fname in [os.path.join(WD, 'data_files', options['loc_file']),
options['samp_file'],
os.path.join(WD, 'data_files', 'specimens.txt')]:
self.assertTrue(os.path.isfile(fname))
def test_cit_magic_with_path(self):
options = {}
#options['input_dir_path'] = os.path.join(WD, 'data_files',
# 'Measurement_Import',
# 'CIT_magic', 'PI47')pppp
options['magfile'] = os.path.join(WD, 'data_files',
'Measurement_Import', 'CIT_magic',
'PI47', 'PI47-.sam')
options['loc_file'] = 'custom_locations.txt'
options['samp_file'] = os.path.join(WD, 'data_files',
'Measurement_Import', 'CIT_magic',
'PI47', 'custom_samples.txt')
options['dir_path'] = os.path.join(WD, 'data_files')
program_ran, outfile = cit_magic.convert(**options)
self.assertTrue(program_ran)
expected_file = os.path.join('measurements.txt')
self.assertEqual(outfile, expected_file)
for fname in [
os.path.join(WD, 'data_files', options['loc_file']),
options['samp_file'],
os.path.join(WD, 'data_files', 'specimens.txt')
]:
self.assertTrue(os.path.isfile(fname))
def test_cit_with_no_files(self):
program_ran, error_message = cit_magic.convert()
self.assertFalse(program_ran)
self.assertEqual(error_message, 'bad sam file name')
def test_cit_with_no_files(self):
program_ran, error_message = cit_magic.convert()
self.assertFalse(program_ran)
self.assertEqual(error_message, 'bad sam file name')