def test_combine(self):
trypsin = enzyme.Protease("trypsin")
gluc = enzyme.Protease("glutamyl endopeptidase")
seq = "PEPTIDER"
self.assertEqual(trypsin.missed_cleavages(seq), 0)
self.assertEqual(gluc.missed_cleavages(seq), 2)
merged = enzyme.Protease.combine(trypsin, gluc)
self.assertEqual(merged.missed_cleavages(seq), 2)
def _prepare_protease(self, protease):
if isinstance(protease, enzyme.Protease):
pass
elif isinstance(protease, basestring):
protease = enzyme.Protease(protease)
elif isinstance(protease, (list, tuple)):
protease = enzyme.Protease.combine(*protease)
return protease
def test_digest(self):
trypsin = enzyme.Protease("trypsin")
for peptide, start, stop, missed in trypsin.cleave(heparanase, 2):
assert missed < 3
if peptide == "KFKNSTYSR":
break
else:
raise AssertionError("Did not produce overlapped digest")
def __init__(self, *args, **kwargs):
super(DigestLayout, self).__init__(*args, **kwargs)
protease = enzyme.Protease(kwargs.get("enzyme", "trypsin"))
self.cleavage_sites = set(i for c in protease.cleave(str(self.protein))
for i in c[1:3] if i != 0)