def test_core_ignore_invalid(self):
"Test Lanthipeptide.core ignores invalid amino acids"
lant = Lanthipeptide(23, 42, 17, 23, 'Class-I')
self.assertEqual('', lant.core)
assert lant.core_analysis is None
lant.core = "MAGICXHAT"
self.assertEqual('MAGICXHAT', lant.core)
assert lant.core_analysis
def test_core(self):
"Test Lanthipeptide.core"
lant = Lanthipeptide(23, 42, 17, 23, 'Class-I')
self.assertEqual('', lant.core)
assert lant.core_analysis is None
lant.core = "MAGICHAT"
self.assertEqual('MAGICHAT', lant.core)
assert lant.core_analysis
def test_result_vec_to_features(self):
"Test lanthipeptides.result_vec_to_features()"
orig_feature = DummyCDS(0, 165)
orig_feature.locus_tag = 'FAKE0001'
vec = Lanthipeptide(17, 23, 42, 23, 'Class-I')
seq = "TAILTAILTAILTAILTAILTAILTAILTAILTAILCC"
vec.core = seq
vec.leader = "HEADHEADHEAD"
motif = result_vec_to_feature(orig_feature, vec)
assert motif.location.start == 0
assert motif.location.end == 165
assert motif.location.strand == 1
assert motif.locus_tag == orig_feature.locus_tag
assert motif.score == 42
assert motif.rodeo_score == 23
assert motif.peptide_class == "lanthipeptide"
assert motif.peptide_subclass == "Class I"
assert motif.lan_bridges == 2
self.assertAlmostEqual(motif.molecular_weight, 3648.6, places=1)
self.assertAlmostEqual(motif.monoisotopic_mass, 3646.3, places=1)
for calc, expected in zip(
motif.alternative_weights,
[3666.6, 3684.6, 3702.7, 3720.7, 3738.7, 3756.7, 3774.7]):
self.assertAlmostEqual(calc, expected, places=1)
assert motif.core == seq
assert motif.leader == vec.leader
new_features = motif.to_biopython()
self.assertEqual(2, len(new_features))
leader, core = new_features
self.assertEqual(0, leader.location.start)
self.assertEqual((12 * 3), leader.location.end)
self.assertEqual(leader.location.strand, 1)
self.assertEqual('CDS_motif', leader.type)
self.assertEqual(orig_feature.locus_tag,
leader.qualifiers['locus_tag'][0])
self.assertEqual(
set([
'leader peptide', 'lanthipeptide',
'predicted leader seq: HEADHEADHEAD'
]), set(leader.qualifiers['note']))
self.assertEqual(leader.location.end, core.location.start)
self.assertEqual(165, core.location.end)
self.assertEqual(1, core.location.strand)
self.assertEqual('CDS_motif', core.type)
expected = [
'core peptide', 'lanthipeptide', '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', 'RODEO score: 23'
]
self.assertEqual(set(expected), set(core.qualifiers['note']))
self.assertEqual(orig_feature.locus_tag,
core.qualifiers['locus_tag'][0])
def test_alternative_weights(self):
"Test Lanthipeptide.alt_weights"
lant = Lanthipeptide(23, 42, 17, 23, 'Class-I')
lant.core = "MAGICHATS"
analysis = ProteinAnalysis("MAGICHATS", monoisotopic=False)
weight = analysis.molecular_weight()
# One Ser/Thr is assumed to be dehydrated, but not the other
weight -= 18.02
self.assertEqual([weight], lant.alternative_weights)
def test_molecular_weight(self):
"Test Lanthipeptide.molecular_weight"
lant = Lanthipeptide(23, 42, 17, 23, 'Class-I')
lant.core = "MAGICHAT"
analysis = ProteinAnalysis("MAGICHAT", monoisotopic=False)
weight = analysis.molecular_weight()
# Thr is assumed to be dehydrated
weight -= 18.02
self.assertAlmostEqual(weight, lant.molecular_weight)
self.assertAlmostEqual(weight, lant._weight)
def test_result_vec_to_features(self):
"Test lanthipeptides.result_vec_to_features()"
orig_feature = DummyCDS(0, 165)
orig_feature.locus_tag = 'FAKE0001'
seq = "TAILTAILTAILTAILTAILTAILTAILTAILTAILCC"
vec = Lanthipeptide(CleavageSiteHit(23, 42, 'Class-I'), 23,
"HEADHEADHEAD", seq)
motif = result_vec_to_feature(orig_feature, vec)
assert motif.location.start == 0
assert motif.location.end == 165
assert motif.location.strand == 1
assert motif.locus_tag == orig_feature.locus_tag
assert motif.score == 42
assert motif.detailed_information.rodeo_score == 23
assert motif.peptide_class == "lanthipeptide"
assert motif.peptide_subclass == "Class I"
assert motif.detailed_information.lan_bridges == 2
self.assertAlmostEqual(motif.molecular_weight, 3648.6, places=1)
self.assertAlmostEqual(motif.monoisotopic_mass, 3646.3, places=1)
for calc, expected in zip(
motif.alternative_weights,
[3666.6, 3684.6, 3702.7, 3720.7, 3738.7, 3756.7, 3774.7]):
self.assertAlmostEqual(calc, expected, places=1)
assert motif.core == seq
assert motif.leader == vec.leader
def test_init(self):
"Test Lanthipeptide instantiation"
lant = Lanthipeptide(23, 42, 17, 23, 'Class-I')
self.assertTrue(isinstance(lant, Lanthipeptide))
self.assertEqual(23, lant.start)
self.assertEqual(42, lant.end)
self.assertEqual(17, lant.score)
self.assertEqual('Class-I', lant.lantype)
self.assertEqual('', lant.core)
with self.assertRaisesRegex(AssertionError,
"calculating weight without a core"):
print(lant.molecular_weight)
def test_number_of_lan_bridges(self):
"Test Lanthipeptide.number_of_lan_bridges"
lant = Lanthipeptide(23, 42, 17, 23, 'Class-I')
lant.core = "MAGICHAT"
self.assertEqual(1, lant.number_of_lan_bridges)
lant.core = "MAGICHATCS"
self.assertEqual(2, lant.number_of_lan_bridges)
lant.core = "MAGICHATCSS"
self.assertEqual(2, lant.number_of_lan_bridges)
lant.core = "MAGICHATCT"
self.assertEqual(2, lant.number_of_lan_bridges)
lant.core = "MAGICHATCCS"
self.assertEqual(2, lant.number_of_lan_bridges)
def setUp(self):
self.lant = Lanthipeptide(CleavageSiteHit(42, 17, 'Class-I'), 23, "HEAD", "MAGICHAT")
def test_repr(self):
"Test Lanthipeptide representation"
lant = Lanthipeptide(23, 42, 17, 23, 'Class-I')
expected = "Lanthipeptide(23..42, 17, 'Class-I', '', -1, -1(-1))"
self.assertEqual(expected, repr(lant))