def test_unknown_index(self):
# TODO - Add SFF file with no index,
# self.assertEqual(str(err), "No index present in this SFF file")
with open("Roche/E3MFGYR02_alt_index_in_middle.sff", "rb") as handle:
try:
values = _sff_find_roche_index(handle)
except ValueError as err:
self.assertTrue(str(err) in ("Unknown magic number '.diy' in SFF index header:\n'.diy1.00'",
"Unknown magic number b'.diy' in SFF index header:\nb'.diy1.00'"))
else:
self.assertTrue(False, "Test _sff_find_roche_index did not raise exception")
def test_unknown_index(self):
# TODO - Add SFF file with no index,
# self.assertEqual(str(err), "No index present in this SFF file")
with open("Roche/E3MFGYR02_alt_index_in_middle.sff", "rb") as handle:
try:
values = _sff_find_roche_index(handle)
except ValueError as err:
self.assertTrue(str(err) in ("Unknown magic number '.diy' in SFF index header:\n'.diy1.00'",
"Unknown magic number b'.diy' in SFF index header:\nb'.diy1.00'"))
else:
self.assertTrue(False, "Test _sff_find_roche_index did not raise exception")
def test_unknown_index(self):
# TODO - Add SFF file with no index,
# self.assertEqual(str(err), "No index present in this SFF file")
with open("Roche/E3MFGYR02_alt_index_in_middle.sff", "rb") as handle:
with self.assertRaises(ValueError) as cm:
values = _sff_find_roche_index(handle)
self.assertIn(
str(cm.exception),
(
"Unknown magic number '.diy' in SFF index header:\n'.diy1.00'",
"Unknown magic number b'.diy' in SFF index header:\nb'.diy1.00'",
),
)
def test_no_index(self):
# Does a lot of work to create a no-index SFF file
# (in the process checking this bit of SffWriter works)
records = list(SeqIO.parse(BytesIO(self.good), "sff"))
with BytesIO() as handle:
writer = SffWriter(handle, index=False)
count = writer.write_file(records)
self.assertEqual(count, len(records))
handle.seek(0)
new = list(SeqIO.parse(handle, "sff"))
self.assertEqual(len(records), len(new))
for a, b in zip(records, new):
self.assertEqual(a.id, b.id)
handle.seek(0)
with self.assertRaises(ValueError) as cm:
values = _sff_find_roche_index(handle)
err = str(cm.exception)
self.assertEqual(err, "No index present in this SFF file")
def test_no_index(self):
# Does a lot of work to create a no-index SFF file
# (in the process checking this bit of SffWriter works)
records = list(SeqIO.parse(BytesIO(self.good), "sff"))
with BytesIO() as handle:
writer = SffWriter(handle, index=False)
count = writer.write_file(records)
self.assertEqual(count, len(records))
handle.seek(0)
new = list(SeqIO.parse(handle, "sff"))
self.assertEqual(len(records), len(new))
for a, b in zip(records, new):
self.assertEqual(a.id, b.id)
handle.seek(0)
try:
values = _sff_find_roche_index(handle)
except ValueError as err:
self.assertEqual(str(err), "No index present in this SFF file")
else:
self.assertTrue(False, "Test _sff_find_roche_index did not raise exception")
