def test_file_invalid(self, invalid_table_alignment):
"""Tests that the invalid alignment files fail properly.
Args:
invalid_table_alignment (pytest.fixture): A parameterized pytest
fixture providing invalid table alignment filenames.
"""
with open(invalid_table_alignment) as in_table:
with pytest.raises(dr.AlignmentIOError):
dr.read_table_alignment_flo(in_table)
def test_stringio_valid(self, valid_table_alignment):
"""Tests that valid table alignment files are loaded correctly.
Tests that the valid alignment files do not fail when loaded into
StringIO objects.
Args:
valid_table_alignment (pytest.fixture): A parameterized pytest
fixture providing valid table alignment filenames.
Raises:
AssertionError: Raised if an exception is thrown when reading.
"""
with open(valid_table_alignment) as in_table:
table_stringio = StringIO()
table_stringio.write(in_table.read())
table_stringio.seek(0)
try:
sequence_list = dr.read_table_alignment_flo(table_stringio)
assert len(sequence_list) > 0
for i in sequence_list:
assert isinstance(i, Sequence)
assert isinstance(i.name, str)
assert len(i.cont_values) > 0
except Exception as e:
print('Raised exception: {}'.format(str(e)))
raise AssertionError(e)
def test_stringio_invalid(self, invalid_table_alignment):
"""Tests that invalid table alignment files cause a failure.
Tests that the invalid alignment files fail properly when loaded into
StringIO objects.
Args:
invalid_table_alignment (pytest.fixture): A parameterized pytest
fixture providing invalid table alignment filenames.
"""
with open(invalid_table_alignment) as in_table:
table_stringio = StringIO()
table_stringio.write(in_table.read())
table_stringio.seek(0)
with pytest.raises(dr.AlignmentIOError):
dr.read_table_alignment_flo(table_stringio)
def test_file_valid(self, valid_table_alignment):
"""Tests that the valid alignment files do not fail.
Args:
valid_table_alignment (pytest.fixture): A parameterized pytest
fixture providing valid table alignment filenames.
"""
with open(valid_table_alignment) as in_table:
try:
sequence_list = dr.read_table_alignment_flo(in_table)
assert len(sequence_list) > 0
for i in sequence_list:
assert isinstance(i, Sequence)
assert isinstance(i.name, string_formats)
assert len(i.cont_values) > 0
except Exception as e:
print('Raised exception: {}'.format(str(e)))
assert False
args.pam_filename))
# Read data
if args.data_format == 'csv':
with open(args.pam_filename) as in_file:
sequences, headers = data_readers.read_csv_alignment_flo(in_file)
elif args.data_format == 'json':
with open(args.pam_filename) as in_file:
sequences, headers = data_readers.read_json_alignment_flo(in_file)
elif args.data_format == 'phylip':
with open(args.pam_filename) as in_file:
sequences = data_readers.read_phylip_alignment_flo(in_file)
headers = None
elif args.data_format == 'table':
with open(args.pam_filename) as in_file:
sequences = data_readers.read_table_alignment_flo(in_file)
headers = None
else:
raise Exception('Unknown data format: {}'.format(args.data_format))
# Get the label annotation column, or None
# label_column = None
# if args.annotate_labels is not None:
# try:
# # Try looking for the string
# label_column = headers.index(args.annotate_labels)
# except:
# try:
# # Treat it as an integer
# label_column = int(args.annotate_labels)
# except: