def test_bad(self):
"""NcbiFastaParser should raise error on bad records if strict"""
# if strict, starting anywhere in the first 15 lines should cause
# errors
for i in range(15):
self.assertRaises(RecordError, list,
NcbiFastaParser(self.nasty[i:]))
# ...but the 16th is OK.
r = list(NcbiFastaParser(self.nasty[15:]))[0]
self.assertEqual(r, ("123", "ucagUCAGtgacNNNN"))
# test that we get what we expect if not strict
r = list(NcbiFastaParser(self.nasty, Sequence, strict=False))
self.assertEqual(len(r), 4)
a, b, c, d = r
self.assertEqual(
(a[1], a[1].info.GI, a[1].info.RefSeq, a[1].info.Description),
("UCAG", ["abc"], ["def"], ""),
)
self.assertEqual(
(b[1], b[1].info.GI, b[1].info.GenBank, b[1].info.Description),
("UUUUCCCC", ["xyz"], ["qwe"], "descr"),
)
self.assertEqual(
(c[1], c[1].info.GI, c[1].info.RefSeq, c[1].info.Description),
("XYZ", ["bad"], ["stuff"], "label"),
)
self.assertEqual(
(d[1], d[1].info.GI, d[1].info.DDBJ, d[1].info.Description),
("ucagUCAGtgacNNNN".upper(), ["123"], ["456"], "desc|with|pipes|"),
)
# ...and when we explicitly supply a constructor
r = list(NcbiFastaParser(self.nasty, Dna, strict=False))
self.assertEqual(len(r), 3)
a, b, c = r
a, b, c = a[1], b[1], c[1]
self.assertEqual(
(a, a.info.GI, a.info.RefSeq, a.info.Description),
("TCAG", ["abc"], ["def"], ""),
)
self.assertEqual(
(b, b.info.GI, b.info.GenBank, b.info.Description),
("TTTTCCCC", ["xyz"], ["qwe"], "descr"),
)
self.assertEqual(
(c, c.info.GI, c.info.DDBJ, c.info.Description),
("tcagTCAGtgacNNNN".upper(), ["123"], ["456"], "desc|with|pipes|"),
)
def test_normal(self):
"""NcbiFastaParser should accept normal record if loose or strict"""
f = list(NcbiFastaParser(self.peptide, Protein))
self.assertEqual(len(f), 2)
a, b = f
a, b = a[1], b[1] # field 0 is the name
self.assertEqual(
a,
"MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNLSEIQNIKSELKYVPKAEQ",
)
self.assertEqual(a.info.GI, ["10047090"])
self.assertEqual(a.info.RefSeq, ["NP_055147.1"])
self.assertEqual(a.info.DDBJ, [])
self.assertEqual(a.info.Description,
"small muscle protein, X-linked [H**o sapiens]")
self.assertEqual(
b,
"MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLYPPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD",
)
self.assertEqual(b.info.GI, ["10047092"])
self.assertEqual(b.info.RefSeq, ["NP_037391.1"])
self.assertEqual(b.info.Description, "neuronal protein [H**o sapiens]")
def test_empty(self):
"""NcbiFastaParser should accept empty input"""
self.assertEqual(list(NcbiFastaParser(self.empty)), [])
self.assertEqual(list(NcbiFastaParser(self.empty, Protein)), [])