def test_core(self):
"Test Thiopeptide.core"
thio = Thiopeptide(20, 31, 32, 51)
thio.core = "MAGICHAT"
self.assertEqual('MAGICHAT', thio.core)
assert thio.core_analysis
thio.core = "MAGICXHAT"
self.assertEqual('MAGICXHAT', thio.core)
assert thio.core_analysis
def test_init(self):
"Test Thiopeptide instantiation"
thio = Thiopeptide(31, 32, 51)
assert isinstance(thio, Thiopeptide)
self.assertEqual(31, thio.end)
self.assertEqual(32, thio.score)
self.assertEqual('', thio.thio_type)
self.assertEqual('', thio.core)
self.assertEqual(51, thio.rodeo_score)
with self.assertRaisesRegex(AssertionError,
"calculating weight without a core"):
print(thio.molecular_weight)
def test_result_vec_to_feature(self):
"Test thiopeptides.result_vec_to_features()"
loc = FeatureLocation(0, 165, strand=1)
orig_feature = DummyCDS(0, 165, locus_tag='FAKE0001')
vec = Thiopeptide(17, 23, 42, 51)
seq = 'SCTSSCTSS'
vec.thio_type = 'Type III'
vec.core = seq
vec.leader = "HEADHEADHEAD"
orig_feature.translation = seq + vec.leader
motif = result_vec_to_feature(orig_feature, vec)
leader, core = motif.to_biopython()
assert loc.start == leader.location.start
assert loc.start + (12 * 3) == leader.location.end
assert loc.strand == leader.location.strand
assert motif.type == 'CDS_motif'
assert motif.peptide_class == "thiopeptide"
assert motif.peptide_subclass == "Type III"
assert orig_feature.locus_tag == motif.locus_tag
assert motif.rodeo_score == 51
assert motif.score == 42
self.assertAlmostEqual(motif.molecular_weight, 861.9, places=1)
assert motif.leader == "HEADHEADHEAD"
assert leader.location.end == core.location.start
assert loc.end == core.location.end
assert loc.strand == core.location.strand
self.assertAlmostEqual(motif.monoisotopic_mass, 861.3, places=1)
assert len(motif.alternative_weights) == 7
for calc, expect in zip(
motif.alternative_weights,
[879.9, 897.9, 916.0, 934.0, 952.0, 970.0, 988.0]):
self.assertAlmostEqual(calc, expect, places=1)
assert not motif.amidation
assert not motif.macrocycle
assert not motif.tail
assert motif.core_features == "Central ring: pyridine trisubstituted"
assert motif.core == "SCTSSCTSS"
def test_macrocycle_size(self):
"Test Thiopeptide._predict_macrocycle"
thio = Thiopeptide(20, 31, 32, 51)
thio.core = "SAAAAAAAASC"
self.assertEqual('26-member', thio.macrocycle)
thio.core = "SAAAAAAAAASSSSSS"
self.assertEqual('35-member', thio.macrocycle)
thio.core = "SDDDDDDDDDSC"
self.assertEqual('29-member', thio.macrocycle)
thio.core = "TAAASDDDDDDDDSCDD"
self.assertEqual('26-member', thio.macrocycle)
def test_repr(self):
"Test Thiopeptide representation"
thio = Thiopeptide(20, 31, 32, 51)
thio.core = "MAGIC"
thio.thio_type = "Type I"
thio.c_cut = "DUMMYC"
thio.macrocycle = "dummy macro"
expected = (
"Thiopeptide(20..31, 32, 'MAGIC', 'Type I', -1.0(-1.0), dummy macro, False, "
"Central ring: pyridine tetrasubstituted (hydroxyl group present); second macrocycle, "
"DUMMYC)")
self.assertEqual(expected, repr(thio))
def test_weights(self):
"Test Thiopeptide.alt_mature_weights"
# includes all weights (even after maturation)
thio = Thiopeptide(23, 42, 17, 51)
thio.core = "MAGICCHATS"
thio.amidation = True
thio.thio_type = "Type I"
mat_weights = thio.mature_alt_weights
weight = mat_weights[0]
mono = mat_weights[1]
alt = mat_weights[2:]
self.assertAlmostEqual(weight, 1051.1623)
self.assertAlmostEqual(mono, 1050.367788)
self.assertAlmostEqual(alt, [1069.1823, 1087.2023])
thio.core = "MAGICCHATS"
thio.amidation = False
thio.thio_type = "Type I"
# reset mature alt weights to calculate them again
thio._mature_alt_weights = []
mat_weights = thio.mature_alt_weights
weight = mat_weights[0]
mono = mat_weights[1]
alt = mat_weights[2:]
self.assertAlmostEqual(weight, 1121.1623)
self.assertAlmostEqual(mono, 1120.367788)
self.assertAlmostEqual(alt, [1139.1823, 1157.2023])
thio.core = "MAGICCHATS"
thio.amidation = True
thio.thio_type = "Type II"
# reset mature alt weights to calculate them again
thio._mature_alt_weights = []
mat_weights = thio.mature_alt_weights
weight = mat_weights[0]
mono = mat_weights[1]
alt = mat_weights[2:]
self.assertAlmostEqual(weight, 1097.1623)
self.assertAlmostEqual(mono, 1096.367788)
self.assertAlmostEqual(alt, [1115.1823, 1133.2023])