def test_result_vec_to_features(self):
"Test lassopeptides.result_vec_to_features()"
orig_feature = DummyCDS(0, 165, strand=1, locus_tag='FAKE0001')
seq = "TAILTAILTAILTAILTAILTAILTAILTAILTAILCCTIP"
vec = Lassopeptide(23, 42, 51, "HEADHEADHEAD", seq)
vec.c_cut = "TIP"
motif = result_vec_to_motif(orig_feature, vec)
assert motif.locus_tag == "FAKE0001"
assert motif.location == orig_feature.location
assert motif.leader == "HEADHEADHEAD"
assert motif.tail == "TIP"
assert motif.core == seq[:-len(motif.tail)]
assert motif.detailed_information.num_bridges == 1
assert motif.peptide_subclass == "Class III"
assert motif.detailed_information.rodeo_score == 51
assert motif.score == 42
assert motif.detailed_information.macrolactam == ""
self.assertAlmostEqual(motif.monoisotopic_mass, 4103.5, delta=1)
self.assertAlmostEqual(motif.molecular_weight, 4106.1, delta=1)
self.assertAlmostEqual(motif.detailed_information.cut_mass,
3792.3,
delta=1)
self.assertAlmostEqual(motif.detailed_information.cut_weight,
3794.7,
delta=1)
def test_molecular_weight(self):
"Test Lassopeptide.molecular_weight"
lasso = Lassopeptide(23, 42, 17, 51, "lead", "MAGICHATTIP")
lasso.c_cut = "TIP"
analysis = ProteinAnalysis("MAGICHATTIP", monoisotopic=False)
cut_analysis = ProteinAnalysis("MAGICHAT", monoisotopic=False)
mw = analysis.molecular_weight() - 18.02
cut_mw = cut_analysis.molecular_weight() - 18.02
self.assertAlmostEqual(mw, lasso.molecular_weight)
self.assertAlmostEqual(cut_mw, lasso.cut_weight)
def test_number_bridges_class(self):
"Test Lassopeptide.number_bridges"
lasso = Lassopeptide(23, 42, 20, 51, "lead", "MAGIXHAT")
self.assertEqual(0, lasso.number_bridges)
self.assertEqual('Class II', lasso.lasso_class)
lasso.core = "CAGIMHAC"
self.assertEqual(1, lasso.number_bridges)
self.assertEqual('Class III', lasso.lasso_class)
lasso.core = "CCCC"
self.assertEqual(2, lasso.number_bridges)
self.assertEqual('Class I', lasso.lasso_class)
def test_init(self):
"Test Lassopeptide instantiation"
lasso = Lassopeptide(42, 17, 51, "", "")
self.assertTrue(isinstance(lasso, Lassopeptide))
self.assertEqual(42, lasso.end)
self.assertEqual(17, lasso.score)
self.assertEqual('Class II', lasso._lassotype)
self.assertEqual('', lasso.core)
self.assertEqual(51, lasso.rodeo_score)
with self.assertRaises(ValueError):
print(lasso.molecular_weight)
def test_macrolactam(self):
"Test Lassopeptide.macrolactam"
lasso = Lassopeptide(23, 42, 20, 51, "lead", "GAAAAADLLLLLLLLL")
self.assertEqual("GAAAAAD", lasso.macrolactam)
def test_core_ignore_invalid(self):
"Test Lassopeptide.core ignores invalid amino acids"
lasso = Lassopeptide(23, 42, 17, 51, "lead", "MAGICXHAT")
assert lasso.core == "MAGICXHAT"
self.assertAlmostEqual(lasso.monoisotopic_mass, 784.3, delta=1)
def test_core(self):
"Test Lassopeptide.core"
lasso = Lassopeptide(23, 42, 17, 51, "lead", "MAGICHAT")
assert lasso.core == "MAGICHAT"
self.assertAlmostEqual(lasso.monoisotopic_mass, 784.3, delta=1)
def test_repr(self):
"Test Lassopeptide representation"
lasso = Lassopeptide(23, 42, 17, 51, "lead", "ABCDEFGHIJKLM")
expected = "Lassopeptide(23..42, 17, 'Class II', 'ABCDEFGHIJKLM', 0, -1(-1), , )"
self.assertEqual(expected, repr(lasso))
