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_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)
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))