def test_compare_categories_numeric_variables(self):
"""Test compare_categories() on numeric methods/input."""
for method in self.num_methods:
compare_categories(self.dm1_fp, self.map1_fp, method,
self.num_categories, self.num_perms, self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
self.assertTrue(len(results) > 0)
def test_compare_categories_morans_i_zeros(self):
"""Test Moran's I on distance matrix with non-diagonal zeros."""
method = 'morans_i'
compare_categories(self.dm2_fp, self.map2_fp, method, ['NumCat'], 999,
self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
self.assertTrue(len(results) > 0)
def test_compare_categories_morans_i_zeros(self):
"""Test Moran's I on distance matrix with non-diagonal zeros."""
method = 'morans_i'
compare_categories(self.dm2_fp, self.map2_fp, method, ['NumCat'], 999,
self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
self.assertTrue(len(results) > 0)
def test_compare_categories_adonis_unique_numeric(self):
"""Test Adonis can run with unique numeric values."""
method = 'adonis'
compare_categories(self.dm1_fp, self.map1_fp, method,
['UniqueNumeric'], 999, self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
self.assertTrue(len(results) > 0)
def test_compare_categories_adonis_unique_numeric(self):
"""Test Adonis can run with unique numeric values."""
method = 'adonis'
compare_categories(self.dm1_fp, self.map1_fp, method,
['UniqueNumeric'], 999, self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
self.assertTrue(len(results) > 0)
def test_compare_categories_categorical_variables(self):
"""Test compare_categories() on categorical methods/input."""
for method in self.cat_methods:
compare_categories(self.dm_fp, self.map_fp, method,
self.cat_categories, self.num_perms, self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
# Make sure the files aren't empty.
self.assertTrue(len(results) > 0)
def test_compare_categories_categorical_variables(self):
"""Test compare_categories() on categorical methods/input."""
for method in self.cat_methods:
compare_categories(self.dm_fp, self.map_fp, method,
self.cat_categories, self.num_perms,
self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
# Make sure the files aren't empty.
self.assertTrue(len(results) > 0)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
out_dir = opts.output_dir
categories = opts.categories.split(",")
# Create the output dir if it doesn't already exist.
try:
if not exists(out_dir):
create_dir(out_dir)
except:
option_parser.error(
"Could not create or access output directory '%s' " "specified with the -o option." % out_dir
)
compare_categories(opts.input_dm, opts.mapping_file, opts.method, categories, opts.num_permutations, out_dir)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
out_dir = opts.output_dir
categories = opts.categories.split(',')
# Create the output dir if it doesn't already exist.
try:
if not exists(out_dir):
create_dir(out_dir)
except:
option_parser.error("Could not create or access output directory '%s' "
"specified with the -o option." % out_dir)
compare_categories(opts.input_dm, opts.mapping_file, opts.method,
categories, opts.num_permutations, out_dir)
def test_compare_categories_invalid_input(self):
"""Test compare_categories() on invalid input that should error out."""
# Non-numeric categories with BEST and Moran's I.
for method in self.num_methods:
self.assertRaises(TypeError, compare_categories, self.dm1_fp,
self.map1_fp, method, self.cat_categories,
self.num_perms, self.test_dir)
# SampleID with all methods.
for method in self.num_methods + self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['SampleID'],
self.num_perms, self.test_dir)
# Single category passed as a string instead of a list of string(s).
for method in self.num_methods + self.cat_methods:
self.assertRaises(TypeError, compare_categories, self.dm1_fp,
self.map1_fp, method, 'SampleID', self.num_perms,
self.test_dir)
# Asymmetric/non-hollow distance matrix.
for method in self.num_methods:
self.assertRaises(DistanceMatrixError, compare_categories,
self.invalid_dm_fp, self.map1_fp, method,
self.num_categories, self.num_perms,
self.test_dir)
for method in self.cat_methods:
self.assertRaises(DistanceMatrixError, compare_categories,
self.invalid_dm_fp, self.map1_fp, method,
self.cat_categories, self.num_perms,
self.test_dir)
# Nonexistent category.
for method in self.num_methods + self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['bar'], self.num_perms,
self.test_dir)
# Unique category values only.
for method in self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['Unique'], self.num_perms,
self.test_dir)
# Only a single category value.
for method in self.cat_methods + self.num_methods:
if method == 'best':
# BEST is okay with this type of category.
compare_categories(self.dm1_fp, self.map1_fp, method,
['Single'], self.num_perms, self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
self.assertTrue(len(results) > 0)
else:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['Single'],
self.num_perms, self.test_dir)
# Bad number of permutations.
for method in self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, self.cat_categories, -42,
self.test_dir)
# Unrecognized method.
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, 'foo', self.cat_categories,
self.num_perms, self.test_dir)
# Samples in dm not found in map.
for method in self.num_methods:
with self.assertRaises(ValueError):
compare_categories(self.dm1_fp, self.missing_sample_map_fp,
method, self.num_categories, self.num_perms,
self.test_dir)
for method in self.cat_methods:
with self.assertRaises(ValueError):
compare_categories(self.dm1_fp, self.missing_sample_map_fp,
method, self.cat_categories, self.num_perms,
self.test_dir)
def test_compare_categories_invalid_input(self):
"""Test compare_categories() on invalid input that should error out."""
# Non-numeric categories with BEST and Moran's I.
for method in self.num_methods:
self.assertRaises(TypeError, compare_categories, self.dm1_fp,
self.map1_fp, method, self.cat_categories, self.num_perms,
self.test_dir)
# SampleID with all methods.
for method in self.num_methods + self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['SampleID'], self.num_perms,
self.test_dir)
# Single category passed as a string instead of a list of string(s).
for method in self.num_methods + self.cat_methods:
self.assertRaises(TypeError, compare_categories, self.dm1_fp,
self.map1_fp, method, 'SampleID', self.num_perms,
self.test_dir)
# Asymmetric/non-hollow distance matrix.
for method in self.num_methods:
self.assertRaises(DistanceMatrixError, compare_categories,
self.invalid_dm_fp, self.map1_fp, method,
self.num_categories, self.num_perms, self.test_dir)
for method in self.cat_methods:
self.assertRaises(DistanceMatrixError, compare_categories,
self.invalid_dm_fp, self.map1_fp, method,
self.cat_categories, self.num_perms, self.test_dir)
# Nonexistent category.
for method in self.num_methods + self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['bar'], self.num_perms,
self.test_dir)
# Unique category values only.
for method in self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['Unique'], self.num_perms,
self.test_dir)
# Only a single category value.
for method in self.cat_methods + self.num_methods:
if method == 'best':
# BEST is okay with this type of category.
compare_categories(self.dm1_fp,
self.map1_fp, method, ['Single'], self.num_perms,
self.test_dir)
results_fp = join(self.test_dir, '%s_results.txt' % method)
self.files_to_remove.append(results_fp)
results_f = open(results_fp, 'U')
results = results_f.readlines()
results_f.close()
self.assertTrue(len(results) > 0)
else:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['Single'], self.num_perms,
self.test_dir)
# Bad number of permutations.
for method in self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, self.cat_categories, -42,
self.test_dir)
# Unrecognized method.
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, 'foo', self.cat_categories,
self.num_perms, self.test_dir)
# Samples in dm not found in map.
for method in self.num_methods:
with self.assertRaises(ValueError):
compare_categories(self.dm1_fp, self.missing_sample_map_fp,
method, self.num_categories, self.num_perms,
self.test_dir)
for method in self.cat_methods:
with self.assertRaises(ValueError):
compare_categories(self.dm1_fp, self.missing_sample_map_fp,
method, self.cat_categories, self.num_perms,
self.test_dir)
def test_compare_categories_invalid_input(self):
"""Test compare_categories() on invalid input that should error out."""
# Non-numeric categories with BIO-ENV and Moran's I.
for method in self.num_methods:
self.assertRaises(TypeError, compare_categories, self.dm1_fp,
self.map1_fp, method, self.cat_categories,
self.num_perms, self.test_dir)
# SampleID with all methods.
for method in self.num_methods + self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['SampleID'],
self.num_perms, self.test_dir)
# Single category passed as a string instead of a list of string(s).
for method in self.num_methods + self.cat_methods:
self.assertRaises(TypeError, compare_categories, self.dm1_fp,
self.map1_fp, method, 'SampleID', self.num_perms,
self.test_dir)
# Asymmetric/non-hollow distance matrix.
for method in self.num_methods:
self.assertRaises(DistanceMatrixError, compare_categories,
self.invalid_dm_fp, self.map1_fp, method,
self.num_categories, self.num_perms,
self.test_dir)
for method in self.cat_methods:
self.assertRaises(DistanceMatrixError, compare_categories,
self.invalid_dm_fp, self.map1_fp, method,
self.cat_categories, self.num_perms,
self.test_dir)
# Nonexistent category.
for method in self.num_methods + self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['bar'], self.num_perms,
self.test_dir)
# Unique category values only.
for method in self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['Unique'], self.num_perms,
self.test_dir)
# Only a single category value.
for method in self.cat_methods + self.num_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['Single'], self.num_perms,
self.test_dir)
# Bad number of permutations.
for method in self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, self.cat_categories, -42,
self.test_dir)
# Unrecognized method.
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, 'foo', self.cat_categories,
self.num_perms, self.test_dir)
# Samples in dm not found in map.
for method in self.num_methods:
with self.assertRaises(ValueError):
compare_categories(self.dm1_fp, self.missing_sample_map_fp,
method, self.num_categories, self.num_perms,
self.test_dir)
for method in self.cat_methods:
with self.assertRaises(ValueError):
compare_categories(self.dm1_fp, self.missing_sample_map_fp,
method, self.cat_categories, self.num_perms,
self.test_dir)
def test_compare_categories_invalid_input(self):
"""Test compare_categories() on invalid input that should error out."""
# Non-numeric categories with BIO-ENV and Moran's I.
for method in self.num_methods:
self.assertRaises(TypeError, compare_categories, self.dm1_fp,
self.map1_fp, method, self.cat_categories, self.num_perms,
self.test_dir)
# SampleID with all methods.
for method in self.num_methods + self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['SampleID'], self.num_perms,
self.test_dir)
# Single category passed as a string instead of a list of string(s).
for method in self.num_methods + self.cat_methods:
self.assertRaises(TypeError, compare_categories, self.dm1_fp,
self.map1_fp, method, 'SampleID', self.num_perms,
self.test_dir)
# Asymmetric/non-hollow distance matrix.
for method in self.num_methods:
self.assertRaises(DistanceMatrixError, compare_categories,
self.invalid_dm_fp, self.map1_fp, method,
self.num_categories, self.num_perms, self.test_dir)
for method in self.cat_methods:
self.assertRaises(DistanceMatrixError, compare_categories,
self.invalid_dm_fp, self.map1_fp, method,
self.cat_categories, self.num_perms, self.test_dir)
# Nonexistent category.
for method in self.num_methods + self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['bar'], self.num_perms,
self.test_dir)
# Unique category values only.
for method in self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['Unique'], self.num_perms,
self.test_dir)
# Only a single category value.
for method in self.cat_methods + self.num_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, ['Single'], self.num_perms,
self.test_dir)
# Bad number of permutations.
for method in self.cat_methods:
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, method, self.cat_categories, -42,
self.test_dir)
# Unrecognized method.
self.assertRaises(ValueError, compare_categories, self.dm1_fp,
self.map1_fp, 'foo', self.cat_categories,
self.num_perms, self.test_dir)
# Samples in dm not found in map.
for method in self.num_methods:
with self.assertRaises(ValueError):
compare_categories(self.dm1_fp, self.missing_sample_map_fp,
method, self.num_categories, self.num_perms,
self.test_dir)
for method in self.cat_methods:
with self.assertRaises(ValueError):
compare_categories(self.dm1_fp, self.missing_sample_map_fp,
method, self.cat_categories, self.num_perms,
self.test_dir)
