def test__guess_seqtype_from_file_genbank_no_header(self):
"Test guessing the sequence type from a genbank file without header"
with open(get_file_path('no_header.gbk'), 'rU') as h:
self.assertEqual("genbank", seqio._guess_seqtype_from_file(h))
h.seek(0)
string_seq = h.read()
self.assertEqual("genbank", seqio._guess_seqtype_from_file(string_seq))
def test__guess_seqtype_from_file_fasta_correct(self):
"Test guessing the sequence type from correct fasta contents"
with open(get_file_path('melanin.fasta'), 'rU') as h:
self.assertEqual("fasta", seqio._guess_seqtype_from_file(h))
h.seek(0)
string_seq = h.read()
self.assertEqual("fasta", seqio._guess_seqtype_from_file(string_seq))
def test__guess_seqtype_from_file_embl_no_header(self):
"Test guessing the sequence type from an embl file without header"
with open(get_file_path('no_header.embl'), 'rU') as h:
self.assertEqual("embl", seqio._guess_seqtype_from_file(h))
h.seek(0)
string_seq = h.read()
self.assertEqual("embl",
seqio._guess_seqtype_from_file(string_seq))
def test__guess_seqtype_from_file_fasta_correct(self):
"Test guessing the sequence type from correct fasta contents"
with open(get_file_path('melanin.fasta'), 'rU') as h:
self.assertEqual("fasta", seqio._guess_seqtype_from_file(h))
h.seek(0)
string_seq = h.read()
self.assertEqual("fasta",
seqio._guess_seqtype_from_file(string_seq))
def test__guess_seqtype_from_file_fasta_no_header_lower_case(self):
"Test guessing the sequence type from a lower case fasta file without header"
with open(get_file_path('no_header.fasta'), 'rU') as h:
string_seq = h.read().lower()
self.assertEqual("fasta", seqio._guess_seqtype_from_file(string_seq))
def test__guess_seqtype_from_file_fasta_no_header_lower_case(self):
"Test guessing the sequence type from a lower case fasta file without header"
with open(get_file_path('no_header.fasta'), 'rU') as h:
string_seq = h.read().lower()
self.assertEqual("fasta",
seqio._guess_seqtype_from_file(string_seq))
