def test_only_labels(self):
"""MinimalRdbParser should return empty list from file w/o seqs"""
#should fail if strict (the default)
self.assertRaises(RecordError, list,
MinimalRdbParser(self.labels, strict=True))
#if not strict, should skip the records
self.assertEqual(list(MinimalRdbParser(self.labels, strict=False)), [])
def test_multiple_bad(self):
"""MinimalRdbParser should complain or skip bad records"""
self.assertRaises(RecordError, list, MinimalRdbParser(self.twogood))
f = list(MinimalRdbParser(self.twogood, strict=False))
self.assertEqual(len(f), 2)
a, b = f
self.assertEqual(a, (['seq:mit'], 'ACU'))
self.assertEqual(b, (['seq:pla'], 'AAA'))
def test_single(self):
"""MinimalRdbParser should read single record as (header,seq) tuple"""
res = list(MinimalRdbParser(self.oneseq))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, (['seq:H.Sapiens'], 'AGUCAUCUAGAUHCAUHC'))
res = list(MinimalRdbParser(self.multiline))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, (['seq:H.Sapiens'], 'AGUCAUUAGAUHCAUHC'))
def test_multiple(self):
"""MinimalRdbParser should read multiple record correctly"""
res = list(MinimalRdbParser(self.threeseq))
self.assertEqual(len(res), 3)
a, b, c = res
self.assertEqual(a, (['seq:bac'], 'AGU'))
self.assertEqual(b, (['seq:mit'], 'ACU'))
self.assertEqual(c, (['seq:pla'], 'AAA'))
def test_empty(self):
"""MinimalRdbParser should return empty list from file w/o seqs"""
self.assertEqual(list(MinimalRdbParser(self.empty)), [])
self.assertEqual(list(MinimalRdbParser(self.nolabels, strict=False)),
[])
self.assertRaises(RecordError, list, MinimalRdbParser(self.nolabels))
def test_strange(self):
"""MRP: handle strange char. according to constr. and strip off '*'"""
f = list(MinimalRdbParser(self.strange))
obs = f[0]
exp = (['seq:bac'], 'ACGUXxAaKkoo---')
self.assertEqual(obs, exp)