Пример #1
0
 def simple_check(self, filename, format, alphabet):
     id_list = [rec.id for rec in \
                SeqIO.parse(open(filename), format, alphabet)]
     rec_dict = SeqIO.indexed_dict(filename, format, alphabet)
     self.assertEqual(set(id_list), set(rec_dict.keys()))
     #This is redundant, I just want to make sure len works:
     self.assertEqual(len(id_list), len(rec_dict))
     #Make sure boolean evaluation works
     self.assertEqual(bool(id_list), bool(rec_dict))
     for key in id_list:
         self.assert_(key in rec_dict)
         self.assertEqual(key, rec_dict[key].id)
         self.assertEqual(key, rec_dict.get(key).id)
     #Check non-existant keys,
     try:
         rec = rec_dict[chr(0)]
         raise ValueError("Accessing a non-existant key should fail")
     except KeyError:
         pass
     self.assertEqual(rec_dict.get(chr(0)), None)
     self.assertEqual(rec_dict.get(chr(0), chr(1)), chr(1))
     #Now check iteritems...
     for key, rec in rec_dict.iteritems():
         self.assert_(key in id_list)
         self.assert_(isinstance(rec, SeqRecord))
         self.assertEqual(rec.id, key)
     #Now check non-defined methods...
     self.assertRaises(NotImplementedError, rec_dict.values)
     self.assertRaises(NotImplementedError, rec_dict.popitem)
     self.assertRaises(NotImplementedError, rec_dict.pop, chr(0))
     self.assertRaises(NotImplementedError, rec_dict.pop, chr(0), chr(1))
     self.assertRaises(NotImplementedError, rec_dict.clear)
     self.assertRaises(NotImplementedError, rec_dict.__setitem__, "X", None)
     self.assertRaises(NotImplementedError, rec_dict.copy)
     self.assertRaises(NotImplementedError, rec_dict.fromkeys, [])
Пример #2
0
 def simple_check(self, filename, format, alphabet) :
     id_list = [rec.id for rec in \
                SeqIO.parse(open(filename), format, alphabet)]
     rec_dict = SeqIO.indexed_dict(filename, format, alphabet)
     self.assertEqual(set(id_list), set(rec_dict.keys()))
     #This is redundant, I just want to make sure len works:
     self.assertEqual(len(id_list), len(rec_dict))
     #Make sure boolean evaluation works
     self.assertEqual(bool(id_list), bool(rec_dict))
     for key in id_list :
         self.assert_(key in rec_dict)
         self.assertEqual(key, rec_dict[key].id)
         self.assertEqual(key, rec_dict.get(key).id)
     #Check non-existant keys,
     try :
         rec = rec_dict[chr(0)]
         raise ValueError("Accessing a non-existant key should fail")
     except KeyError :
         pass
     self.assertEqual(rec_dict.get(chr(0)), None)
     self.assertEqual(rec_dict.get(chr(0), chr(1)), chr(1))
     #Now check iteritems...
     for key, rec in rec_dict.iteritems() :
         self.assert_(key in id_list)
         self.assert_(isinstance(rec, SeqRecord))
         self.assertEqual(rec.id, key)
     #Now check non-defined methods...
     self.assertRaises(NotImplementedError, rec_dict.values)
     self.assertRaises(NotImplementedError, rec_dict.popitem)
     self.assertRaises(NotImplementedError, rec_dict.pop, chr(0))
     self.assertRaises(NotImplementedError, rec_dict.pop, chr(0), chr(1))
     self.assertRaises(NotImplementedError, rec_dict.clear)
     self.assertRaises(NotImplementedError, rec_dict.__setitem__, "X", None)
     self.assertRaises(NotImplementedError, rec_dict.copy)
     self.assertRaises(NotImplementedError, rec_dict.fromkeys, [])