def test__get_seqtype_from_ext(self):
"Test guessing the sequence type from the file extension for handle input"
gbk_h = DummyHandle("test.gbk")
gb_h = DummyHandle("test.gb")
genbank_h = DummyHandle("test.genbank")
gbff_h = DummyHandle("test.gbff")
embl_h = DummyHandle("test.embl")
emb_h = DummyHandle("test.emb")
fa_h = DummyHandle("test.fa")
fasta_h = DummyHandle("test.fasta")
fna_h = DummyHandle("test.fna")
faa_h = DummyHandle("test.faa")
fas_h = DummyHandle("test.fas")
gbk_gz_h = DummyHandle("test.gbk.gz")
gb_gz_h = DummyHandle("test.gb.gz")
genbank_gz_h = DummyHandle("test.genbank.gz")
gbff_gz_h = DummyHandle("test.gbff.gz")
invalid_h = DummyHandle("test.invalid")
for handle in (gbk_h, gb_h, genbank_h, gbff_h):
self.assertEqual("genbank", seqio._get_seqtype_from_ext(handle))
for handle in (embl_h, emb_h):
self.assertEqual("embl", seqio._get_seqtype_from_ext(handle))
for handle in (fa_h, fasta_h, fna_h, faa_h, fas_h):
self.assertEqual("fasta", seqio._get_seqtype_from_ext(handle))
for handle in (gbk_gz_h, gb_gz_h, genbank_gz_h, gbff_gz_h):
self.assertEqual("gz-genbank", seqio._get_seqtype_from_ext(handle))
self.assertRaises(ValueError, seqio._get_seqtype_from_ext, invalid_h)
def ensure_type_for_extension(self, extension, expected_type):
handle = DummyHandle("test.%s" % extension)
self.assertEqual(expected_type, seqio._get_seqtype_from_ext(handle))
# and test cases where the whole filename *is* the extension
handle = DummyHandle(extension)
self.assertEqual(expected_type, seqio._get_seqtype_from_ext(handle))
def ensure_type_for_extension(self, extension, expected_type):
handle = DummyHandle("test.%s" % extension)
self.assertEqual(expected_type, seqio._get_seqtype_from_ext(handle))
# and test cases where the whole filename *is* the extension
handle = DummyHandle(extension)
self.assertEqual(expected_type, seqio._get_seqtype_from_ext(handle))
def test__get_seqtype_from_ext_string(self):
"Test guessing the sequence type from the file extension for string input"
for string in ("test.gbk", "test.gb", "test.genbank", "test.gbff"):
self.assertEqual("genbank", seqio._get_seqtype_from_ext(string))
for string in ("test.embl", "test.emb"):
self.assertEqual("embl", seqio._get_seqtype_from_ext(string))
for string in ("test.fa", "test.fasta", "test.fna", "test.faa", "test.fas"):
self.assertEqual("fasta", seqio._get_seqtype_from_ext(string))
for string in ("test.gbk.gz", "test.gb.gz", "test.genbank.gz", "test.gbff.gz"):
self.assertEqual("gz-genbank", seqio._get_seqtype_from_ext(string))
self.assertRaises(ValueError, seqio._get_seqtype_from_ext, "test.invalid")
def test__get_seqtype_from_ext_string(self):
"Test guessing the sequence type from the file extension for string input"
for string in ("test.gbk", "test.gb", "test.genbank", "test.gbff"):
self.assertEqual("genbank", seqio._get_seqtype_from_ext(string))
for string in ("test.embl", "test.emb"):
self.assertEqual("embl", seqio._get_seqtype_from_ext(string))
for string in ("test.fa", "test.fasta", "test.fna", "test.faa",
"test.fas"):
self.assertEqual("fasta", seqio._get_seqtype_from_ext(string))
for string in ("test.gbk.gz", "test.gb.gz", "test.genbank.gz",
"test.gbff.gz"):
self.assertEqual("gz-genbank", seqio._get_seqtype_from_ext(string))
self.assertRaises(ValueError, seqio._get_seqtype_from_ext,
"test.invalid")
