def test_prot_mixedcase(self):
fd_test = self._prep_fd(['p-mixedcase'])
fd_true = smof.FileDescription()
fd_true.ntype['prot'] += 1
fd_true.ncase['mixedcase'] += 1
self.assertTrue(self._equal_counts(fd_true, fd_test))
def test_illegal(self):
fd_test = self._prep_fd(['illegal'])
fd_true = smof.FileDescription()
fd_true.ntype['illegal'] += 1
fd_true.ncase['uppercase'] += 1
self.assertTrue(self._equal_counts(fd_true, fd_test))
def test_prot_gapped(self):
fd_test = self._prep_fd(['p-gapped'])
fd_true = smof.FileDescription()
fd_true.ntype['prot'] += 1
fd_true.ncase['uppercase'] += 1
fd_true.ufeat['gapped'] += 1
self.assertTrue(self._equal_counts(fd_true, fd_test))
def test_prot_initial_met(self):
fd_test = self._prep_fd(['p-initial-Met'])
fd_true = smof.FileDescription()
fd_true.ntype['prot'] += 1
fd_true.ncase['uppercase'] += 1
fd_true.pfeat['initial-Met'] += 1
self.assertTrue(self._equal_counts(fd_true, fd_test))
def test_prot_terminal_stop(self):
fd_test = self._prep_fd(['p-terminal-stop'])
fd_true = smof.FileDescription()
fd_true.ntype['prot'] += 1
fd_true.ncase['uppercase'] += 1
fd_true.pfeat['terminal-stop'] += 1
self.assertTrue(self._equal_counts(fd_true, fd_test))
def test_prot_selenocysteine(self):
fd_test = self._prep_fd(['p-selenocysteine'])
fd_true = smof.FileDescription()
fd_true.ntype['prot'] += 1
fd_true.ncase['uppercase'] += 1
fd_true.pfeat['selenocysteine'] += 1
self.assertTrue(self._equal_counts(fd_true, fd_test))
def _prep_fd(self, keys):
fd = smof.FileDescription()
for key in keys:
seq = smof.FSeq(header=key, seq=self.seqs[key])
fd.add_seq(seq)
return (fd)