def test_fasta_badqual_id(self):
wk = FastaIterator(seq=self.fastas, qual=self.bad_qual_id)
gen = wk()
# default behavior is to sliently ignore
exp_ids = ['1', '2', '4', '5']
obs_ids = [r['SequenceID'] for r in gen]
self.assertEqual(obs_ids, exp_ids)
def test_fasta_gen(self):
wk = FastaIterator(seq=self.fastas)
gen = wk()
exp1 = {
'SequenceID': '1',
'Sequence': 'aattggcc',
'Qual': None,
'QualID': None
}
exp2 = {
'SequenceID': '2',
'Sequence': 'aattaatt',
'Qual': None,
'QualID': None
}
exp3 = {
'SequenceID': '3',
'Sequence': 'atat',
'Qual': None,
'QualID': None
}
exp4 = {
'SequenceID': '4',
'Sequence': 'attatt',
'Qual': None,
'QualID': None
}
exp5 = {
'SequenceID': '5',
'Sequence': 'ggccc',
'Qual': None,
'QualID': None
}
obs1 = next(gen)
self.assertEqual(obs1, exp1)
self.assertFalse(wk.failed)
obs2 = next(gen)
self.assertEqual(obs2, exp2)
self.assertFalse(wk.failed)
obs3 = next(gen)
self.assertEqual(obs3, exp3)
self.assertFalse(wk.failed)
obs4 = next(gen)
self.assertEqual(obs4, exp4)
self.assertFalse(wk.failed)
obs5 = next(gen)
self.assertEqual(obs5, exp5)
self.assertFalse(wk.failed)
def test_fasta_qual(self):
wk = FastaIterator(seq=self.fastas, qual=self.quals)
gen = wk()
exp1 = {
'SequenceID': '1',
'Sequence': 'aattggcc',
'Qual': arange(1, 9),
'QualID': '1'
}
exp2 = {
'SequenceID': '2',
'Sequence': 'aattaatt',
'QualID': '2',
'Qual': arange(1, 9)[::-1]
}
exp3 = {
'SequenceID': '3',
'Sequence': 'atat',
'Qual': arange(1, 5),
'QualID': '3'
}
exp4 = {
'SequenceID': '4',
'Sequence': 'attatt',
'Qual': arange(1, 7),
'QualID': '4'
}
exp5 = {
'SequenceID': '5',
'Sequence': 'ggccc',
'Qual': arange(1, 6),
'QualID': '5'
}
obs1 = next(gen)
self.assertTrue((obs1['Qual'] == exp1['Qual']).all())
obs1.pop('Qual')
exp1.pop('Qual')
self.assertEqual(obs1, exp1)
self.assertFalse(wk.failed)
obs2 = next(gen)
self.assertTrue((obs2['Qual'] == exp2['Qual']).all())
obs2.pop('Qual')
exp2.pop('Qual')
self.assertEqual(obs2, exp2)
self.assertFalse(wk.failed)
obs3 = next(gen)
self.assertTrue((obs3['Qual'] == exp3['Qual']).all())
obs3.pop('Qual')
exp3.pop('Qual')
self.assertEqual(obs3, exp3)
self.assertFalse(wk.failed)
obs4 = next(gen)
self.assertTrue((obs4['Qual'] == exp4['Qual']).all())
obs4.pop('Qual')
exp4.pop('Qual')
self.assertEqual(obs4, exp4)
self.assertFalse(wk.failed)
obs5 = next(gen)
self.assertTrue((obs5['Qual'] == exp5['Qual']).all())
obs5.pop('Qual')
exp5.pop('Qual')
self.assertEqual(obs5, exp5)
self.assertFalse(wk.failed)