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))