def test_check_bad_chars(self):
"""check_bad_chars should return string of errors for invalid fields"""
field_types = {
'bc': 'uid',
'ph': float,
'sample': 'uid',
'ctl': ['Yes', 'No']
}
good_data = array([
['sample', 'bc', 'ph', 'ctl', 'x'],
['x', 'x', '3', 'Yes', 'x'],
['y', 'y', '4', 'No', 'x'],
])
self.assertEqual(check_bad_chars((good_data, field_types)),
((good_data, field_types), ''))
bad_vals = array([
['sample', 'bc', 'ph', 'ctl', 'x'],
['x', 'x!', '3', 'Yes', 'x'],
['y', 'y', '>', 'No', 'x'],
])
self.assertEqual(check_bad_chars((bad_vals, field_types)), (
(array([['sample', 'bc', 'ph', 'ctl', 'x'],
['x', 'x_', '3', 'Yes', 'x'], ['y', 'y', '_', 'No', 'x']],
dtype='|S6'), {
'sample': 'uid',
'ctl': ['Yes', 'No'],
'ph': float,
'bc': 'uid'
}),
'Removed bad chars from cell x! (now x_) in sample id x, col bc. Location (row, column):\t0,1\nRemoved bad chars from cell > (now _) in sample id y, col ph. Location (row, column):\t1,2'
))
def test_check_bad_chars(self):
"""check_bad_chars should return string of errors for invalid fields"""
field_types = {'bc':'uid','ph':float,'sample':'uid','ctl':['Yes','No']}
good_data = array([
['sample','bc','ph','ctl','x'],
['x','x','3','Yes','x'],
['y','y','4','No','x'],
])
self.assertEqual(check_bad_chars((good_data, field_types)),
((good_data, field_types),''))
bad_vals = array([
['sample','bc','ph','ctl','x'],
['x','x!','3','Yes','x'],
['y','y','>','No','x'],
])
self.assertEqual(check_bad_chars((bad_vals, field_types)),((array([['sample', 'bc', 'ph', 'ctl', 'x'],['x', 'x_', '3', 'Yes', 'x'], ['y', 'y', '_', 'No', 'x']], dtype='|S6'), {'sample': 'uid', 'ctl': ['Yes', 'No'], 'ph': float, 'bc': 'uid'}), 'Removed bad chars from cell x! (now x_) in sample id x, col bc. Location (row, column):\t0,1\nRemoved bad chars from cell > (now _) in sample id y, col ph. Location (row, column):\t1,2'))
def test_check_bad_chars_meins(self):
""" Should enforce MEINS compliance in SampleID column (first column)
"""
field_types = {'bc':'uid','ph':float,'sample':'uid','ctl':['Yes','No']}
meins_compliant_data = array([
['#SampleID','Barcode','LinkerPrimerSequence','Treatment','Description'],
['Sample.1','AATCT','CCGTA','Yes','x'],
['TestSubject','ATCCT','CCGTA','No_placebo','x'],
])
self.assertEqual(check_bad_chars((meins_compliant_data, field_types)),
((meins_compliant_data, field_types),''))
non_meins_compliant_data = array([
['#SampleID','Barcode','LinkerPrimerSequence','Treatment','Description'],
['Sample_1','AATCT','CCGTA','Yes','x'],
['TestSubject','ATCCT','CCGTA','No','x'],
])
self.assertEqual(check_bad_chars((non_meins_compliant_data, field_types)),\
((array([['#SampleID', 'Barcode', 'LinkerPrimerSequence', 'Treatment','Description'], ['Sample.1', 'AATCT', 'CCGTA', 'Yes', 'x'], ['TestSubject', 'ATCCT', 'CCGTA', 'No', 'x']], dtype='|S20'), {'sample': 'uid', 'ctl': ['Yes', 'No'], 'ph': float, 'bc': 'uid'}), 'Removed bad chars from cell Sample_1 (now Sample.1) in sample id Sample.1, col #SampleID. Location (row, column):\t0,0'))
def test_check_bad_chars_handles_primer_pool(self):
""" Should allow commas in primer field for primer pools """
field_types = {'bc':'uid','LinkerPrimerSequence':float,
'sample':'uid','ctl':['Yes','No']}
good_data = array([
['sample','bc','LinkerPrimerSequence','ctl','x'],
['x','x','ATTCG,AYCGA','Yes','x'],
['y','y','ACSGGAYT','No','x'],
])
self.assertEqual(check_bad_chars((good_data, field_types)),
((good_data, field_types),''))
