def test_core_ignore_invalid(self):
"Test Lantipeptide.core ignores invalid amino acids"
lant = Lantipeptide(23, 42, 17, 'Class-I')
self.assertEqual('', lant.core)
self.assertFalse(hasattr(lant, 'core_analysis'))
lant.core = "MAGICXHAT"
self.assertEqual('MAGICHAT', lant.core)
self.assertTrue(hasattr(lant, 'core_analysis'))
def test_core(self):
"Test Lantipeptide.core"
lant = Lantipeptide(23, 42, 17, 'Class-I')
self.assertEqual('', lant.core)
self.assertFalse(hasattr(lant, 'core_analysis'))
lant.core = "MAGICHAT"
self.assertEqual('MAGICHAT', lant.core)
self.assertTrue(hasattr(lant, 'core_analysis'))
def test_alternative_weights(self):
"Test Lantipeptide.alt_weights"
lant = Lantipeptide(23, 42, 17, 'Class-I')
lant.core = "MAGICHATS"
analysis = ProteinAnalysis("MAGICHATS", monoisotopic=False)
mw = analysis.molecular_weight()
# One Ser/Thr is assumed to be dehydrated, but not the other
mw -= 18.02
self.assertEqual([mw], lant.alternative_weights)
def test_number_of_lan_bridges(self):
"Test Lantipeptide.number_of_lan_bridges"
lant = Lantipeptide(23, 42, 17, 'Class-I')
lant.core = "MAGICHAT"
self.assertEqual(-1, lant._lan_bridges)
self.assertEqual(1, lant.number_of_lan_bridges)
lant._lan_bridges = 2
self.assertEqual(2, lant._lan_bridges)
self.assertEqual(2, lant.number_of_lan_bridges)
def test_molecular_weight(self):
"Test Lantipeptide.molecular_weight"
lant = Lantipeptide(23, 42, 17, 'Class-I')
lant.core = "MAGICHAT"
analysis = ProteinAnalysis("MAGICHAT", monoisotopic=False)
mw = analysis.molecular_weight()
# Thr is assumed to be dehydrated
mw -= 18.02
self.assertAlmostEqual(mw, lant.molecular_weight)
self.assertAlmostEqual(mw, lant._weight)
lant._weight = 42
self.assertEqual(42, lant.molecular_weight)
def test_result_vec_to_features(self):
"Test lantipeptides.result_vec_to_features()"
loc = FeatureLocation(0, 165, strand=1)
orig_feature = SeqFeature(loc, 'CDS')
orig_feature.qualifiers['locus_tag'] = ['FAKE0001']
vec = Lantipeptide(17, 23, 42, 'Class-I')
seq = "TAILTAILTAILTAILTAILTAILTAILTAILTAILCC"
vec.core = seq
vec.leader = "HEADHEADHEAD"
new_features = result_vec_to_features(orig_feature, vec)
self.assertEqual(2, len(new_features))
leader, core = new_features
self.assertEqual(loc.start, leader.location.start)
self.assertEqual(loc.start + (23 * 3), leader.location.end)
self.assertEqual(loc.strand, leader.location.strand)
self.assertEqual('CDS_motif', leader.type)
self.assertEqual(orig_feature.qualifiers['locus_tag'],
leader.qualifiers['locus_tag'])
self.assertEqual(
['leader peptide', 'predicted leader seq: HEADHEADHEAD'],
leader.qualifiers['note'])
self.assertEqual(leader.location.end, core.location.start)
self.assertEqual(loc.end, core.location.end)
self.assertEqual(loc.strand, core.location.strand)
self.assertEqual('CDS_motif', core.type)
expected = [
'core peptide', 'monoisotopic mass: 3646.3',
'molecular weight: 3648.6',
'alternative weights: 3666.6; 3684.6; 3702.7; 3720.7; 3738.7; 3756.7; 3774.7',
'number of bridges: 2',
'predicted core seq: TAILTAILTAILTAILTAILTAILTAILTAILTAILCC',
'predicted class: Class-I', 'score: 42.00'
]
self.assertEqual(expected, core.qualifiers['note'])
self.assertEqual(orig_feature.qualifiers['locus_tag'],
core.qualifiers['locus_tag'])