def test_file_invalid(self, invalid_csv_alignment):
"""Tests that the invalid alignment files fail properly.
Args:
invalid_csv_alignment (pytest.fixture): A parameterized pytest
fixture providing invalid csv alignment filenames.
"""
with open(invalid_csv_alignment) as in_csv:
with pytest.raises(dr.AlignmentIOError):
dr.read_csv_alignment_flo(in_csv)
def test_stringio_valid(self, valid_csv_alignment):
"""Tests that alignments are read properly with valid input data.
Tests that the valid alignment files do not fail when loaded into
StringIO objects.
Args:
valid_csv_alignment (pytest.fixture): A parameterized pytest
fixture providing valid csv alignment filenames.
Raises:
AssertionError: Raised if an exception is thrown when reading.
"""
with open(valid_csv_alignment) as in_csv:
csv_stringio = StringIO()
csv_stringio.write(in_csv.read())
csv_stringio.seek(0)
try:
(sequence_list,
headers) = dr.read_csv_alignment_flo(csv_stringio)
assert len(headers) > 0
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_csv_alignment):
"""Tests that invalid alignment files cause the proper failure.
Tests that the invalid alignment files fail properly when loaded into
StringIO objects.
Args:
invalid_csv_alignment (pytest.fixture): A parameterized pytest
fixture providing invalid csv alignment filenames.
"""
with open(invalid_csv_alignment) as in_csv:
csv_stringio = StringIO()
csv_stringio.write(in_csv.read())
csv_stringio.seek(0)
with pytest.raises(dr.AlignmentIOError):
dr.read_csv_alignment_flo(csv_stringio)
def test_file_valid(self, valid_csv_alignment):
"""Tests that the valid alignment files do not fail.
Args:
valid_csv_alignment (pytest.fixture): A parameterized pytest
fixture providing valid csv alignment filenames.
"""
with open(valid_csv_alignment) as in_csv:
try:
sequence_list, headers = dr.read_csv_alignment_flo(in_csv)
assert len(headers) > 0
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
else:
nrand = int(args.number_permutations)
print(nrand)
# Check that input files exist
if not os.path.exists(args.in_tree_filename):
raise IOError('Input tree {} does not exist'.format(
args.in_tree_filename))
if not os.path.exists(args.pam_filename):
raise IOError('Input data file {} does not exist'.format(
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