def test_euclidean_perfect(self):
observed = compare_sinks(self.mpm1, self.mpm1, 'euclidean')
expected_ids = ['sink1', 'sink2', 'sink3', 'sink4', 'sink5', 'sink6']
expected_values = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
expected = pd.DataFrame(expected_values, index=expected_ids,
columns=['Euclidean distance'])
assert_data_frame_almost_equal(observed, expected)
def test_default_valid_multi_line(self):
fp = get_data_path('blast7_default_multi_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject2', 70.00, 5.0, 0.0, 0.0, 7.0,
60.0, 3.0, 100.0, 9e-05, 10.5],
['query1', 'subject2', 30.00, 8.0, 0.0, 0.0, 6.0,
15.0, 1.0, 100.0, 0.053, 12.0],
['query1', 'subject2', 90.00, 2.0, 0.0, 0.0, 9.0,
35.0, 2.0, 100.0, 0.002, 8.3]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
fp = get_data_path('legacy9_multi_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject1', 90.00, 7.0, 1.0, 0.0, 0.0,
8.0, 4.0, 10.0, 1e-05, 15.5],
['query1', 'subject1', 70.00, 8.0, 0.0, 1.0, 0.0,
9.0, 5.0, 7.0, 0.231, 7.8],
['query1', 'subject1', 90.00, 5.0, 1.0, 1.0, 0.0,
0.0, 2.0, 10.0, 0.022, 13.0]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_ancom_percentiles(self):
table = pd.DataFrame([[12, 11],
[9, 11],
[1, 11],
[22, 100],
[20, 53],
[23, 1]],
index=['s1', 's2', 's3', 's4', 's5', 's6'],
columns=['b1', 'b2'])
grouping = pd.Series(['a', 'a', 'a', 'b', 'b', 'b'],
index=['s1', 's2', 's3', 's4', 's5', 's6'])
percentiles = [0.0, 25.0, 50.0, 75.0, 100.0]
groups = ['a', 'b']
tuples = [(p, g) for g in groups for p in percentiles]
exp_mi = pd.MultiIndex.from_tuples(tuples,
names=['Percentile', 'Group'])
exp_data = np.array(
[[1.0, 11.0], [5.0, 11.0], [9.0, 11.0], [10.5, 11.0], [12.0, 11.0],
[20.0, 1.0], [21.0, 27.0], [22.0, 53.0], [22.5, 76.5],
[23.0, 100.0]])
exp = pd.DataFrame(exp_data.T, columns=exp_mi, index=['b1', 'b2'])
result = ancom(table, grouping)[1]
assert_data_frame_almost_equal(result, exp)
def test_init_default_parameters(self):
seq = ExampleGrammaredSequence('.-ABCXYZ')
npt.assert_equal(seq.values, np.array('.-ABCXYZ', dtype='c'))
self.assertEqual(seq.metadata, {})
assert_data_frame_almost_equal(seq.positional_metadata,
pd.DataFrame(index=range(8)))
def test_ancom_basic_counts_swapped(self):
result = ancom(self.table8, self.cats8)
exp = pd.DataFrame({'W': np.array([5, 5, 2, 2, 2, 2, 2]),
'reject': np.array([True, True, False, False,
False, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_default_valid_multi_line(self):
fp = get_data_path('blast7_default_multi_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject2', 70.00, 5.0, 0.0, 0.0, 7.0,
60.0, 3.0, 100.0, 9e-05, 10.5],
['query1', 'subject2', 30.00, 8.0, 0.0, 0.0, 6.0,
15.0, 1.0, 100.0, 0.053, 12.0],
['query1', 'subject2', 90.00, 2.0, 0.0, 0.0, 9.0,
35.0, 2.0, 100.0, 0.002, 8.3]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
fp = get_data_path('legacy9_multi_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject1', 90.00, 7.0, 1.0, 0.0, 0.0,
8.0, 4.0, 10.0, 1e-05, 15.5],
['query1', 'subject1', 70.00, 8.0, 0.0, 1.0, 0.0,
9.0, 5.0, 7.0, 0.231, 7.8],
['query1', 'subject1', 90.00, 5.0, 1.0, 1.0, 0.0,
0.0, 2.0, 10.0, 0.022, 13.0]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_to_data_frame_3x3(self):
df = self.dm_3x3.to_data_frame()
exp = pd.DataFrame([[0.0, 0.01, 4.2],
[0.01, 0.0, 12.0],
[4.2, 12.0, 0.0]],
index=['a', 'b', 'c'], columns=['a', 'b', 'c'])
assert_data_frame_almost_equal(df, exp)
def test_ancom_alpha(self):
result = ancom(self.table1, self.cats1, alpha=0.5)
exp = pd.DataFrame({'W': np.array([6, 6, 4, 5, 5, 4, 2]),
'reject': np.array([True, True, False, True,
True, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_to_data_frame_3x3(self):
df = self.dm_3x3.to_data_frame()
exp = pd.DataFrame(
[[0.0, 0.01, 4.2], [0.01, 0.0, 12.0], [4.2, 12.0, 0.0]],
index=['a', 'b', 'c'],
columns=['a', 'b', 'c'])
assert_data_frame_almost_equal(df, exp)
def test_id_lookup(self):
# Matrices have mismatched IDs but a lookup is provided.
self.minx_dm_extra.ids = ['a', 'b', 'c', 'foo']
self.minz_dm_extra.ids = ['d', 'e', 'f', 'bar']
lookup = {'a': '0', 'b': '1', 'c': '2', 'foo': 'foo',
'd': '0', 'e': '1', 'f': '2', 'bar': 'bar',
'0': '0', '1': '1', '2': '2'}
x = self.minx_dm_extra.filter(['b', 'a', 'foo', 'c'])
y = self.miny_dm.filter(['0', '2', '1'])
z = self.minz_dm_extra.filter(['bar', 'e', 'f', 'd'])
x_copy = x.copy()
y_copy = y.copy()
z_copy = z.copy()
np.random.seed(0)
obs = pwmantel((x, y, z), alternative='greater', strict=False,
lookup=lookup)
assert_data_frame_almost_equal(
obs,
self.exp_results_reordered_distance_matrices)
# Make sure the inputs aren't modified.
self.assertEqual(x, x_copy)
self.assertEqual(y, y_copy)
self.assertEqual(z, z_copy)
def test_scale_single_column(self):
df = pd.DataFrame([[1], [0], [2]], index=['A', 'B', 'C'],
columns=['foo'])
exp = pd.DataFrame([[0.0], [-1.0], [1.0]], index=['A', 'B', 'C'],
columns=['foo'])
obs = _scale(df)
assert_data_frame_almost_equal(obs, exp)
def test_ancom_no_signal(self):
result = ancom(self.table3,
self.cats3,
multiple_comparisons_correction=None)
exp = pd.DataFrame({'W': np.array([0]*7),
'reject': np.array([False]*7, dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_ancom_alpha(self):
result = ancom(self.table1, self.cats1, alpha=0.5)
exp = pd.DataFrame({'W': np.array([6, 6, 4, 5, 5, 4, 2]),
'reject': np.array([True, True, False, True,
True, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_absolute_difference(self):
mpm1 = {
'Unknown': {
'sink1': 0.25
},
'Source1': {
'sink1': 0.50
},
'Source2': {
'sink1': 0.25
}
}
mpm1 = pd.DataFrame(mpm1)
mpm2 = {
'Unknown': {
'sink1': 0.1
},
'Source2': {
'sink1': 0.8
},
'Source1': {
'sink1': 0.1
}
}
mpm2 = pd.DataFrame(mpm2)
observed = compare_sinks(mpm1, mpm2, 'absolute_difference')
expected_ids = ['sink1']
# expected values computed by hand
expected_values = [(0.4, 0.55, 0.15)]
expected = pd.DataFrame(expected_values,
index=expected_ids,
columns=['Source1', 'Source2', 'Unknown'])
assert_data_frame_almost_equal(observed.sort_index(axis=1),
expected.sort_index(axis=1))
def test_permutative_f_scaled(self):
test_table = pd.DataFrame(
closure([[12, 11, 10, 10, 10, 10, 10],
[9, 11, 12, 10, 10, 10, 10],
[1, 11, 10, 11, 10, 5, 9],
[2, 11, 10, 11, 10, 5, 9],
[221, 210, 9, 10, 10, 10, 10],
[220, 210, 9, 10, 10, 10, 10],
[200, 220, 10, 10, 13, 10, 10],
[230, 210, 14, 10, 10, 10, 10]]),
index=['s1', 's2', 's3', 's4',
's5', 's6', 's7', 's8'],
columns=['b1', 'b2', 'b3', 'b4', 'b5', 'b6', 'b7'])
test_cats = pd.Series([0, 0, 0, 0, 1, 1, 1, 1],
index=['s1', 's2', 's3', 's4',
's5', 's6', 's7', 's8'])
np.random.seed(0)
original_table = copy.deepcopy(test_table)
original_cats = copy.deepcopy(test_cats)
result = ancom(test_table, test_cats,
significance_test='permutative-anova')
# Test to make sure that the input table hasn't be altered
assert_data_frame_almost_equal(original_table, test_table)
# Test to make sure that the input table hasn't be altered
pdt.assert_series_equal(original_cats, test_cats)
exp = pd.DataFrame({'W': np.array([5, 5, 2, 2, 2, 2, 2]),
'reject': np.array([True, True, False, False,
False, False, False],
dtype=bool)},
index=['b1', 'b2', 'b3', 'b4',
'b5', 'b6', 'b7'])
assert_data_frame_almost_equal(result, exp)
def test_ancom_percentiles(self):
table = pd.DataFrame([[12, 11],
[9, 11],
[1, 11],
[22, 100],
[20, 53],
[23, 1]],
index=['s1', 's2', 's3', 's4', 's5', 's6'],
columns=['b1', 'b2'])
grouping = pd.Series(['a', 'a', 'a', 'b', 'b', 'b'],
index=['s1', 's2', 's3', 's4', 's5', 's6'])
percentiles = [0.0, 25.0, 50.0, 75.0, 100.0]
groups = ['a', 'b']
tuples = [(p, g) for g in groups for p in percentiles]
exp_mi = pd.MultiIndex.from_tuples(tuples,
names=['Percentile', 'Group'])
exp_data = np.array(
[[1.0, 11.0], [5.0, 11.0], [9.0, 11.0], [10.5, 11.0], [12.0, 11.0],
[20.0, 1.0], [21.0, 27.0], [22.0, 53.0], [22.5, 76.5],
[23.0, 100.0]])
exp = pd.DataFrame(exp_data.T, columns=exp_mi, index=['b1', 'b2'])
result = ancom(table, grouping)[1]
assert_data_frame_almost_equal(result, exp)
def test_ancom_no_signal(self):
result = ancom(self.table3,
self.cats3,
multiple_comparisons_correction=None)
exp = pd.DataFrame({'W': np.array([0]*7),
'reject': np.array([False]*7, dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_id_lookup(self):
# Matrices have mismatched IDs but a lookup is provided.
self.minx_dm_extra.ids = ['a', 'b', 'c', 'foo']
self.minz_dm_extra.ids = ['d', 'e', 'f', 'bar']
lookup = {'a': '0', 'b': '1', 'c': '2', 'foo': 'foo',
'd': '0', 'e': '1', 'f': '2', 'bar': 'bar',
'0': '0', '1': '1', '2': '2'}
x = self.minx_dm_extra.filter(['b', 'a', 'foo', 'c'])
y = self.miny_dm.filter(['0', '2', '1'])
z = self.minz_dm_extra.filter(['bar', 'e', 'f', 'd'])
x_copy = x.copy()
y_copy = y.copy()
z_copy = z.copy()
np.random.seed(0)
obs = pwmantel((x, y, z), alternative='greater', strict=False,
lookup=lookup)
assert_data_frame_almost_equal(
obs,
self.exp_results_reordered_distance_matrices)
# Make sure the inputs aren't modified.
self.assertEqual(x, x_copy)
self.assertEqual(y, y_copy)
self.assertEqual(z, z_copy)
def test_bioenv_different_column_order(self):
# Specifying columns in a different order will change the row labels in
# the results data frame as the column subsets will be reordered, but
# the actual results (e.g., correlation coefficients) shouldn't change.
obs = bioenv(self.dm, self.df, columns=self.cols[::-1])
assert_data_frame_almost_equal(obs,
self.exp_results_different_column_order)
def test_not_equal(self):
unequal_dfs = [
self.df,
# floating point error too large to be "almost equal"
pd.DataFrame({'foo': [42, 42.001, np.nan, 0],
'bar': ['a', 'b', 'cd', 'e']}),
# extra NaN
pd.DataFrame({'foo': [42, np.nan, np.nan, 0],
'bar': ['a', 'b', 'cd', 'e']}),
# different column order
pd.DataFrame(self.df, columns=['foo', 'bar']),
# different index order
pd.DataFrame(self.df, index=np.arange(4)[::-1]),
# different index type
pd.DataFrame(self.df, index=np.arange(4).astype(float)),
# various forms of "empty" DataFrames that are not equivalent
pd.DataFrame(),
pd.DataFrame(index=np.arange(10)),
pd.DataFrame(columns=np.arange(10)),
pd.DataFrame(index=np.arange(10), columns=np.arange(10)),
pd.DataFrame(index=np.arange(9)),
pd.DataFrame(columns=np.arange(9)),
pd.DataFrame(index=np.arange(9), columns=np.arange(9))
]
# each df should compare equal to itself
for df in unequal_dfs:
assert_data_frame_almost_equal(df, df)
# every pair of dfs should not compare equal. use permutations instead
# of combinations to test that comparing df1 to df2 and df2 to df1 are
# both not equal
for df1, df2 in itertools.permutations(unequal_dfs, 2):
with self.assertRaises(AssertionError):
assert_data_frame_almost_equal(df1, df2)
def test_ancom_percentiles_alt_categories(self):
table = pd.DataFrame([[12], [9], [1], [22], [20], [23]],
index=['s1', 's2', 's3', 's4', 's5', 's6'],
columns=['b1'])
grouping = pd.Series(['a', 'a', 'c', 'b', 'b', 'c'],
index=['s1', 's2', 's3', 's4', 's5', 's6'])
percentiles = [0.0, 25.0, 50.0, 75.0, 100.0]
groups = ['a', 'b', 'c']
tuples = [(p, g) for g in groups for p in percentiles]
exp_mi = pd.MultiIndex.from_tuples(tuples,
names=['Percentile', 'Group'])
exp_data = np.array([
[9.0],
[9.75],
[10.5],
[11.25],
[12.0], # a
[20.0],
[20.5],
[21.0],
[21.5],
[22.0], # b
[1.0],
[6.5],
[12.0],
[17.5],
[23.0]
]) # c
exp = pd.DataFrame(exp_data.T, columns=exp_mi, index=['b1'])
result = ancom(table, grouping, percentiles=percentiles)[1]
assert_data_frame_almost_equal(result, exp)
def test_init_default_parameters(self):
seq = ExampleGrammaredSequence('.-ABCXYZ')
npt.assert_equal(seq.values, np.array('.-ABCXYZ', dtype='c'))
self.assertEqual(seq.metadata, {})
assert_data_frame_almost_equal(seq.positional_metadata,
pd.DataFrame(index=range(8)))
def test_pearsonr(self):
mpm1 = {
'Unknown': {
'sink1': 0.25
},
'Source1': {
'sink1': 0.50
},
'Source2': {
'sink1': 0.25
}
}
mpm1 = pd.DataFrame(mpm1)
mpm2 = {
'Unknown': {
'sink1': 0.1
},
'Source1': {
'sink1': 0.1
},
'Source2': {
'sink1': 0.8
}
}
mpm2 = pd.DataFrame(mpm2)
observed = compare_sinks(mpm1, mpm2, 'pearson')
expected_ids = ['sink1']
# expected values computed by calling scipy.stats.pearsonr directly
expected_values = [(-0.5, 2. / 3)]
expected = pd.DataFrame(expected_values,
index=expected_ids,
columns=['Pearson r', 'p'])
assert_data_frame_almost_equal(observed, expected)
def test_default_valid_single_line(self):
fp = get_data_path('blast7_default_single_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([[
'query1', 'subject2', 100.00, 8.0, 0.0, 0.0, 1.0, 8.0, 3.0, 10.0,
9e-05, 16.9
]],
columns=[
'qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'
])
assert_data_frame_almost_equal(df, exp)
fp = get_data_path('legacy9_single_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([[
'query1', 'subject1', 90.00, 7.0, 1.0, 0.0, 0.0, 8.0, 4.0, 10.0,
1e-05, 15.5
]],
columns=[
'qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'
])
assert_data_frame_almost_equal(df, exp)
def test_euclidean(self):
mpm1 = {
'Unknown': {
'sink1': 0.25
},
'Source1': {
'sink1': 0.50
},
'Source2': {
'sink1': 0.25
}
}
mpm1 = pd.DataFrame(mpm1)
mpm2 = {
'Unknown': {
'sink1': 0.1
},
'Source1': {
'sink1': 0.1
},
'Source2': {
'sink1': 0.8
}
}
mpm2 = pd.DataFrame(mpm2)
observed = compare_sinks(mpm1, mpm2, 'euclidean')
expected_ids = ['sink1']
# expected values computed by calling
# scipy.stats.spatial.distance.euclidean directly
expected_values = [0.6964194]
expected = pd.DataFrame(expected_values,
index=expected_ids,
columns=['Euclidean distance'])
assert_data_frame_almost_equal(observed, expected)
def test_ancom_basic_counts_swapped(self):
result = ancom(self.table8, self.cats8)
exp = pd.DataFrame({'W': np.array([5, 5, 2, 2, 2, 2, 2]),
'reject': np.array([True, True, False, False,
False, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_euclidean_perfect(self):
observed = compare_sinks(self.mpm1, self.mpm1, 'euclidean')
expected_ids = ['sink1', 'sink2', 'sink3', 'sink4', 'sink5', 'sink6']
expected_values = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
expected = pd.DataFrame(expected_values,
index=expected_ids,
columns=['Euclidean distance'])
assert_data_frame_almost_equal(observed, expected)
def test_ancom_theta(self):
result = ancom(self.table1, self.cats1, theta=0.3)
exp = pd.DataFrame(
{'W': np.array([5, 5, 2, 2, 2, 2, 2]),
'Reject null hypothesis': np.array([True, True, False, False,
False, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result[0], exp)
def test_ancom_theta(self):
result = ancom(self.table1, self.cats1, theta=0.3)
exp = pd.DataFrame(
{'W': np.array([5, 5, 2, 2, 2, 2, 2]),
'Reject null hypothesis': np.array([True, True, False, False,
False, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result[0], exp)
def test_ancom_multiple_comparisons(self):
result = ancom(self.table1,
self.cats1,
multiple_comparisons_correction='holm-bonferroni',
significance_test=scipy.stats.mannwhitneyu)
exp = pd.DataFrame({'W': np.array([0]*7),
'reject': np.array([False]*7, dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_custom_valid_single_line(self):
fp = get_data_path("blast7_custom_single_line")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 100.00, 100.00, 8.0, 0.0, 16.9, 8.0,
'PAAWWWWW']],
columns=['qseqid', 'ppos', 'pident', 'length',
'sgi', 'bitscore', 'qend', 'qseq'])
assert_data_frame_almost_equal(df, exp)
def test_custom_valid_single_line(self):
fp = get_data_path("blast7_custom_single_line")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 100.00, 100.00, 8.0, 0.0, 16.9, 8.0,
'PAAWWWWW']],
columns=['qseqid', 'ppos', 'pident', 'length',
'sgi', 'bitscore', 'qend', 'qseq'])
assert_data_frame_almost_equal(df, exp)
def test_ancom_no_percentiles(self):
table = pd.DataFrame([[12], [9], [1], [22], [20], [23]],
index=['s1', 's2', 's3', 's4', 's5', 's6'],
columns=['b1'])
grouping = pd.Series(['a', 'a', 'a', 'b', 'b', 'b'],
index=['s1', 's2', 's3', 's4', 's5', 's6'])
result = ancom(table, grouping, percentiles=[])[1]
assert_data_frame_almost_equal(result, pd.DataFrame())
def test_ancom_multiple_comparisons(self):
result = ancom(self.table1,
self.cats1,
multiple_comparisons_correction='holm-bonferroni',
significance_test=scipy.stats.mannwhitneyu)
exp = pd.DataFrame({'W': np.array([0]*7),
'reject': np.array([False]*7, dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_minimal_compatible_input_with_labels(self):
np.random.seed(0)
obs = pwmantel(self.min_dms, alternative='greater',
labels=('minx', 'miny', 'minz'))
assert_data_frame_almost_equal(
obs,
self.exp_results_minimal_with_labels)
def test_minimal_compatible_input_with_labels(self):
np.random.seed(0)
obs = pwmantel(self.min_dms,
alternative='greater',
labels=('minx', 'miny', 'minz'))
assert_data_frame_almost_equal(obs,
self.exp_results_minimal_with_labels)
def test_bioenv_different_column_order(self):
# Specifying columns in a different order will change the row labels in
# the results data frame as the column subsets will be reordered, but
# the actual results (e.g., correlation coefficients) shouldn't change.
obs = bioenv(self.dm, self.df, columns=self.cols[::-1])
assert_data_frame_almost_equal(
obs,
self.exp_results_different_column_order)
def test_pearson_perfect(self):
observed = compare_sinks(self.mpm1, self.mpm1, 'pearson')
expected_ids = ['sink1', 'sink2', 'sink3', 'sink4', 'sink5', 'sink6']
expected_values = [(1.0, 0.0), (1.0, 0.0), (1.0, 0.0), (1.0, 0.0),
(1.0, 0.0), (1.0, 0.0)]
expected = pd.DataFrame(expected_values, index=expected_ids,
columns=['Pearson r', 'p'])
assert_data_frame_almost_equal(observed, expected)
def test_filepaths_as_input(self):
dms = [
get_data_path('dm.txt'),
get_data_path('dm2.txt'),
]
np.random.seed(0)
obs = pwmantel(dms)
assert_data_frame_almost_equal(obs, self.exp_results_dm_dm2)
def test_default_valid_single_line(self):
fp = get_data_path('blast6_default_single_line')
df = _blast6_to_data_frame(fp, default_columns=True)
exp = pd.DataFrame([['query1', 'subject2', 75.0, 8.0, 2.0, 0.0, 1.0,
8.0, 2.0, 9.0, 0.06, 11.5]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_filepaths_as_input(self):
dms = [
get_data_path('dm.txt'),
get_data_path('dm2.txt'),
]
np.random.seed(0)
obs = pwmantel(dms)
assert_data_frame_almost_equal(obs, self.exp_results_dm_dm2)
def test_bioenv_all_columns_implicit(self):
# Test with all columns in data frame (implicitly).
obs = bioenv(self.dm, self.df)
assert_data_frame_almost_equal(obs, self.exp_results)
# Should get the same results if order of rows/cols in distance matrix
# is changed.
obs = bioenv(self.dm_reordered, self.df)
assert_data_frame_almost_equal(obs, self.exp_results)
def test_custom_valid_single_line(self):
fp = get_data_path('blast6_custom_single_line')
df = _blast6_to_data_frame(fp, columns=['qacc', 'qseq', 'btop',
'sframe', 'ppos',
'positive', 'gaps'])
exp = pd.DataFrame([['query1', 'PAAWWWWW', 8.0, 1.0, 100.00, 8.0,
0.0]], columns=['qacc', 'qseq', 'btop', 'sframe',
'ppos', 'positive', 'gaps'])
assert_data_frame_almost_equal(df, exp)
def test_ancom_letter_categories(self):
result = ancom(self.table7,
self.cats7,
multiple_comparisons_correction=None)
exp = pd.DataFrame({'W': np.array([5, 3, 3, 2, 2, 5, 2]),
'reject': np.array([True, False, False, False,
False, True, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_ancom_alpha(self):
result = ancom(self.table1, self.cats1,
multiple_comparisons_correction=None, alpha=0.5)
exp = pd.DataFrame(
{'W': np.array([6, 6, 4, 5, 5, 4, 2]),
'Reject null hypothesis': np.array([True, True, False, True,
True, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result[0], exp)
def test_ancom_letter_categories(self):
result = ancom(self.table7,
self.cats7,
multiple_comparisons_correction=None)
exp = pd.DataFrame({'W': np.array([5, 3, 3, 2, 2, 5, 2]),
'reject': np.array([True, False, False, False,
False, True, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_ancom_alpha(self):
result = ancom(self.table1, self.cats1,
multiple_comparisons_correction=None, alpha=0.5)
exp = pd.DataFrame(
{'W': np.array([6, 6, 4, 5, 5, 4, 2]),
'Reject null hypothesis': np.array([True, True, False, True,
True, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result[0], exp)
def test_ancom_noncontiguous(self):
result = ancom(self.table5,
self.cats5,
multiple_comparisons_correction=None)
exp = pd.DataFrame({'W': np.array([6, 2, 2, 2, 2, 6, 2]),
'reject': np.array([True, False, False, False,
False, True, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_bioenv_all_columns_implicit(self):
# Test with all columns in data frame (implicitly).
obs = bioenv(self.dm, self.df)
assert_data_frame_almost_equal(obs, self.exp_results)
# Should get the same results if order of rows/cols in distance matrix
# is changed.
obs = bioenv(self.dm_reordered, self.df)
assert_data_frame_almost_equal(obs, self.exp_results)
def test_scale_single_column(self):
df = pd.DataFrame([[1], [0], [2]],
index=['A', 'B', 'C'],
columns=['foo'])
exp = pd.DataFrame([[0.0], [-1.0], [1.0]],
index=['A', 'B', 'C'],
columns=['foo'])
obs = _scale(df)
assert_data_frame_almost_equal(obs, exp)
def test_ancom_noncontiguous(self):
result = ancom(self.table5,
self.cats5,
multiple_comparisons_correction=None)
exp = pd.DataFrame({'W': np.array([6, 2, 2, 2, 2, 6, 2]),
'reject': np.array([True, False, False, False,
False, True, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_pearson_perfect(self):
observed = compare_sinks(self.mpm1, self.mpm1, 'pearson')
expected_ids = ['sink1', 'sink2', 'sink3', 'sink4', 'sink5', 'sink6']
expected_values = [(1.0, 0.0), (1.0, 0.0), (1.0, 0.0), (1.0, 0.0),
(1.0, 0.0), (1.0, 0.0)]
expected = pd.DataFrame(expected_values,
index=expected_ids,
columns=['Pearson r', 'p'])
assert_data_frame_almost_equal(observed, expected)
def test_ancom_unbalanced(self):
result = ancom(self.table6,
self.cats6,
multiple_comparisons_correction=None)
exp = pd.DataFrame(
{'W': np.array([5, 3, 3, 2, 2, 5, 2]),
'Reject null hypothesis': np.array([True, False, False, False,
False, True, False],
dtype=bool)})
assert_data_frame_almost_equal(result[0], exp)
def test_ancom_alternative_test(self):
result = ancom(self.table1,
self.cats1,
multiple_comparisons_correction=None,
significance_test=scipy.stats.ttest_ind)
exp = pd.DataFrame({'W': np.array([5, 5, 2, 2, 2, 2, 2]),
'reject': np.array([True, True, False, False,
False, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_bioenv_all_columns_explicit(self):
# Test with all columns being specified.
obs = bioenv(self.dm, self.df, columns=self.cols)
assert_data_frame_almost_equal(obs, self.exp_results)
# Test against a data frame that has an extra non-numeric column and
# some of the rows and columns reordered (we should get the same
# result since we're specifying the same columns in the same order).
obs = bioenv(self.dm, self.df_extra_column, columns=self.cols)
assert_data_frame_almost_equal(obs, self.exp_results)
def test_ancom_alternative_test(self):
result = ancom(self.table1,
self.cats1,
multiple_comparisons_correction=None,
significance_test=scipy.stats.ttest_ind)
exp = pd.DataFrame({'W': np.array([5, 5, 2, 2, 2, 2, 2]),
'reject': np.array([True, True, False, False,
False, False, False],
dtype=bool)})
assert_data_frame_almost_equal(result, exp)
def test_init_nondefault_parameters(self):
seq = ExampleGrammaredSequence(
'.-ABCXYZ',
metadata={'id': 'foo'},
positional_metadata={'quality': range(8)})
npt.assert_equal(seq.values, np.array('.-ABCXYZ', dtype='c'))
self.assertEqual(seq.metadata, {'id': 'foo'})
assert_data_frame_almost_equal(seq.positional_metadata,
pd.DataFrame({'quality': range(8)}))
def test_custom_valid_mixed_nans(self):
fp = get_data_path("blast7_custom_mixed_nans")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([[0.0, np.nan, 8.0, 13.0, 1.0, 1.0, np.nan,
'subject2'],
[np.nan, 0.0, 8.0, np.nan, 1.0, 1.0, 'query1',
np.nan]],
columns=['qgi', 'sgi', 'qlen', 'slen', 'qframe',
'sframe', 'qseqid', 'sseqid'])
assert_data_frame_almost_equal(df, exp)
def test_ancom_unbalanced(self):
result = ancom(self.table6,
self.cats6,
multiple_comparisons_correction=None)
exp = pd.DataFrame(
{'W': np.array([5, 3, 3, 2, 2, 5, 2]),
'Reject null hypothesis': np.array([True, False, False, False,
False, True, False],
dtype=bool)})
assert_data_frame_almost_equal(result[0], exp)
def test_bioenv_all_columns_explicit(self):
# Test with all columns being specified.
obs = bioenv(self.dm, self.df, columns=self.cols)
assert_data_frame_almost_equal(obs, self.exp_results)
# Test against a data frame that has an extra non-numeric column and
# some of the rows and columns reordered (we should get the same
# result since we're specifying the same columns in the same order).
obs = bioenv(self.dm, self.df_extra_column, columns=self.cols)
assert_data_frame_almost_equal(obs, self.exp_results)