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_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_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_read_fasta_no_header(self):
"Test reading a fasta record without header"
with open(get_file_path('no_header.fasta'), 'rU') as h:
# plain BioPython reading should fail
self.assertRaises(ValueError, seqio.read, h)
h.seek(0)
# robust reading should work
record = seqio.read(h, robust=True)
self.assertEqual("DUMMY", record.id)
def test_read_fasta_no_header(self):
"Test reading a fasta record without header"
with open(get_file_path('no_header.fasta'), 'rU') as h:
# plain BioPython reading should fail
self.assertRaises(ValueError, seqio.read, h)
h.seek(0)
# robust reading should work
record = seqio.read(h, robust=True)
self.assertEqual("DUMMY", record.id)
def test_parse_fasta_no_header(self):
"Test parsing a fasta record without header"
with open(get_file_path('no_header.fasta'), 'rU') as h:
# plain BioPython parsing should fail
records = list(seqio.parse(h))
self.assertEqual(0, len(records))
h.seek(0)
# robust parsing should work
records = list(seqio.parse(h, robust=True))
self.assertEqual(1, len(records))
def test_parse_fasta_no_header(self):
"Test parsing a fasta record without header"
with open(get_file_path('no_header.fasta'), 'rU') as h:
# plain BioPython parsing should fail
records = list(seqio.parse(h))
self.assertEqual(0, len(records))
h.seek(0)
# robust parsing should work
records = list(seqio.parse(h, robust=True))
self.assertEqual(1, len(records))
def test_read_fasta_valid(self):
"Test reading a valid fasta record"
with open(get_file_path('melanin.fasta'), 'rU') as h:
record = seqio.read(h)
self.assertEqual("AB070938", record.id)
def test_read_embl_valid(self):
"Test reading a valid embl record"
with open(get_file_path('melanin.embl'), 'rU') as h:
record = seqio.read(h)
self.assertEqual("AB070938.1", record.id)
def test_parse_fasta_valid(self):
"Test parsing a valid fasta record"
with open(get_file_path('melanin.fasta'), 'rU') as h:
records = list(seqio.parse(h))
self.assertEqual(1, len(records))
def test_parse_genbank_valid(self):
"Test parsing a valid genbank record"
with open(get_file_path('melanin.gbk'), 'rU') as h:
records = list(seqio.parse(h))
self.assertEqual(1, len(records))
def test_read_embl_valid(self):
"Test reading a valid embl record"
with open(get_file_path('melanin.embl'), 'rU') as h:
record = seqio.read(h)
self.assertEqual("AB070938.1", record.id)
def test_parse_genbank_path(self):
"Test parsing a gzipped GenBank file specified by path"
fname = get_file_path('melanin.gbk.gz')
records = list(seqio.parse(fname))
self.assertEqual(1, len(records))
def test_parse_genbank(self):
"Test parsing a gzipped GenBank file"
with open(get_file_path('melanin.gbk.gz'), 'rb') as h:
records = list(seqio.parse(h))
self.assertEqual(1, len(records))
def test_read_genbank_path(self):
"Test reading a gzipped GenBank file specified by path"
fname = get_file_path('melanin.gbk.gz')
record = seqio.read(fname)
self.assertEqual("AB070938.1", record.id)
def test_parse_genbank_path(self):
"Test parsing a gzipped GenBank file specified by path"
fname = get_file_path('melanin.gbk.gz')
records = list(seqio.parse(fname))
self.assertEqual(1, len(records))
def test_read_genbank(self):
"Test reading a gzipped GenBank file"
with open(get_file_path('melanin.gbk.gz'), 'rb') as h:
record = seqio.read(h)
self.assertEqual("AB070938.1", record.id)
def test_parse_genbank(self):
"Test parsing a gzipped GenBank file"
with open(get_file_path('melanin.gbk.gz'), 'rb') as h:
records = list(seqio.parse(h))
self.assertEqual(1, len(records))
def test_read_fasta_valid(self):
"Test reading a valid fasta record"
with open(get_file_path('melanin.fasta'), 'rU') as h:
record = seqio.read(h)
self.assertEqual("AB070938", record.id)
def test_read_genbank(self):
"Test reading a gzipped GenBank file"
with open(get_file_path('melanin.gbk.gz'), 'rb') as h:
record = seqio.read(h)
self.assertEqual("AB070938.1", record.id)
def test_parse_fasta_valid(self):
"Test parsing a valid fasta record"
with open(get_file_path('melanin.fasta'), 'rU') as h:
records = list(seqio.parse(h))
self.assertEqual(1, len(records))
def test_read_genbank_path(self):
"Test reading a gzipped GenBank file specified by path"
fname = get_file_path('melanin.gbk.gz')
record = seqio.read(fname)
self.assertEqual("AB070938.1", record.id)
def test_parse_genbank_valid(self):
"Test parsing a valid genbank record"
with open(get_file_path('melanin.gbk'), 'rU') as h:
records = list(seqio.parse(h))
self.assertEqual(1, len(records))
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))