def setUp(self):
"""Define some standard Organizers for testing"""
self.Empty = Organizer([])
self.a = Filter('a', {None: [find_any('a')]})
self.b = Filter('b', {None: [find_any('b')]})
self.Ab_org = Organizer([self.a, self.b])
lsu = Filter('LSU',{None:[exclude_if_more('N',5)],\
'Gene':[find_any(['LSU'])]})
ssu = Filter('SSU',{None:[exclude_if_more('N',5)],\
'Gene':[find_any(['SSU'])]})
self.Gene_org = Organizer([lsu, ssu])
self.Ab_seq = ['aa', 'bb', 'abab', 'cc', '']
self.seq1 = Sequence('ACGU', {'Gene': 'LSU'})
self.seq2 = Sequence('ACGUACGU', {'Gene': 'SSU'})
self.seq3 = Sequence('ACGUNNNNNN', {'Gene': 'LSU'})
self.seq4 = Sequence('ACGUNNNNNN', {'Gene': 'SSU'})
self.seq5 = Sequence('ACGU', {})
self.seq6 = Sequence('', {})
self.seq7 = Sequence('ACGU', {'Gene': 'unit'})
self.Gene_seq = [self.seq1,self.seq2,self.seq3,self.seq4,\
self.seq5,self.seq6,self.seq7]
f = Filter('valid',{None:[find_all('AGCU'),find_no('N')],\
'Gene':[find_any(['LSU'])]})
self.Mult_func_org = Organizer([f])
def test_init_full(self):
"""Organizer should init correctly with multiple functions"""
org = Organizer([self.a, self.b])
self.assertEqual(org[0], self.a)
self.assertEqual(org[1], self.b)
self.assertEqual(len(org), 2)