本文整理汇总了Python中qiime2.metadata.Metadata类的典型用法代码示例。如果您正苦于以下问题：Python Metadata类的具体用法？Python Metadata怎么用？Python Metadata使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Metadata类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_various_numbers
def test_various_numbers(self):
numbers = [
0.0, -0.0, np.nan, 1.0, 42.0, -33.0, 1e-10, 1.5e15, 0.0003, -4.234,
# This last number should be rounded because it exceeds 15 digits
# of precision.
12.34567891234567
]
index = pd.Index(['id1', 'id2', 'id3', 'id4', 'id5', 'id6', 'id7',
'id8', 'id9', 'id10', 'id11'], name='ID')
md = Metadata(pd.DataFrame({'numbers': numbers}, index=index))
md.save(self.filepath)
with open(self.filepath, 'r') as fh:
obs = fh.read()
exp = (
"ID\tnumbers\n"
"#q2:types\tnumeric\n"
"id1\t0\n"
"id2\t-0\n"
"id3\t\n"
"id4\t1\n"
"id5\t42\n"
"id6\t-33\n"
"id7\t1e-10\n"
"id8\t1.5e+15\n"
"id9\t0.0003\n"
"id10\t-4.234\n"
"id11\t12.3456789123457\n"
)
self.assertEqual(obs, exp)示例2: test_qiime1_empty_mapping_file
def test_qiime1_empty_mapping_file(self):
fp = pkg_resources.resource_filename(
'qiime2.metadata.tests', 'data/qiime1-empty.tsv')
with self.assertRaisesRegex(MetadataFileError,
'at least one ID.*empty'):
Metadata.load(fp)示例3: test_invalid_header
def test_invalid_header(self):
fp = get_data_path('invalid/invalid-header.tsv')
with self.assertRaisesRegex(MetadataFileError,
'unrecognized ID column name.*'
'invalid_id_header'):
Metadata.load(fp)示例4: test_unrecognized_column_type_in_directive
def test_unrecognized_column_type_in_directive(self):
fp = get_data_path('invalid/unrecognized-column-type.tsv')
with self.assertRaisesRegex(MetadataFileError,
'col2.*unrecognized column type.*foo.*'
'#q2:types directive'):
Metadata.load(fp)示例5: test_unrecognized_directive
def test_unrecognized_directive(self):
fp = get_data_path('invalid/unrecognized-directive.tsv')
with self.assertRaisesRegex(MetadataFileError,
'Unrecognized directive.*#q2:foo.*'
'#q2:types directive is supported'):
Metadata.load(fp)示例6: test_duplicate_columns_self_merge
def test_duplicate_columns_self_merge(self):
md = Metadata(pd.DataFrame(
{'a': [1, 2], 'b': [3, 4]},
index=pd.Index(['id1', 'id2'], name='id')))
with self.assertRaisesRegex(ValueError, "columns overlap: 'a', 'b'"):
md.merge(md)示例7: test_data_longer_than_header
def test_data_longer_than_header(self):
fp = get_data_path('invalid/data-longer-than-header.tsv')
with self.assertRaisesRegex(MetadataFileError,
'row has 5 cells.*header declares 4 '
'cells'):
Metadata.load(fp)示例8: test_path_is_directory
def test_path_is_directory(self):
fp = get_data_path('valid')
with self.assertRaisesRegex(MetadataFileError,
"path points to something other than a "
"file"):
Metadata.load(fp)示例9: test_comments_and_empty_rows_only
def test_comments_and_empty_rows_only(self):
fp = get_data_path('invalid/comments-and-empty-rows-only.tsv')
with self.assertRaisesRegex(MetadataFileError,
'locate header.*only of comments or empty '
'rows'):
Metadata.load(fp)示例10: test_index_and_column_merge_order
def test_index_and_column_merge_order(self):
md1 = Metadata(pd.DataFrame(
[[1], [2], [3], [4]],
index=pd.Index(['id1', 'id2', 'id3', 'id4'], name='id'),
columns=['a']))
md2 = Metadata(pd.DataFrame(
[[5], [6], [7]], index=pd.Index(['id4', 'id3', 'id1'], name='id'),
columns=['b']))
md3 = Metadata(pd.DataFrame(
[[8], [9], [10]], index=pd.Index(['id1', 'id4', 'id3'], name='id'),
columns=['c']))
obs = md1.merge(md2, md3)
exp = Metadata(pd.DataFrame(
[[1, 7, 8], [3, 6, 10], [4, 5, 9]],
index=pd.Index(['id1', 'id3', 'id4'], name='id'),
columns=['a', 'b', 'c']))
self.assertEqual(obs, exp)
# Merging in different order produces different ID/column order.
obs = md2.merge(md1, md3)
exp = Metadata(pd.DataFrame(
[[5, 4, 9], [6, 3, 10], [7, 1, 8]],
index=pd.Index(['id4', 'id3', 'id1'], name='id'),
columns=['b', 'a', 'c']))
self.assertEqual(obs, exp)示例11: test_directive_before_header
def test_directive_before_header(self):
fp = get_data_path('invalid/directive-before-header.tsv')
with self.assertRaisesRegex(MetadataFileError,
'directive.*#q2:types.*searching for '
'header'):
Metadata.load(fp)示例12: test_ids_and_column_names_as_numeric_strings
def test_ids_and_column_names_as_numeric_strings(self):
index = pd.Index(['0.000001', '0.004000', '0.000000'],
dtype=object, name='id')
columns = ['42.0', '1000', '-4.2']
data = [
[2.0, 'b', 2.5],
[1.0, 'b', 4.2],
[3.0, 'c', -9.999]
]
df = pd.DataFrame(data, index=index, columns=columns)
md = Metadata(df)
md.save(self.filepath)
with open(self.filepath, 'r') as fh:
obs = fh.read()
exp = (
"id\t42.0\t1000\t-4.2\n"
"#q2:types\tnumeric\tcategorical\tnumeric\n"
"0.000001\t2\tb\t2.5\n"
"0.004000\t1\tb\t4.2\n"
"0.000000\t3\tc\t-9.999\n"
)
self.assertEqual(obs, exp)示例13: test_column_types_override_directive_not_convertible_to_numeric
def test_column_types_override_directive_not_convertible_to_numeric(self):
fp = get_data_path('valid/simple-with-directive.tsv')
with self.assertRaisesRegex(MetadataFileError,
"column 'col3' to numeric.*could not be "
"interpreted as numeric: 'bar', 'foo'"):
Metadata.load(fp, column_types={'col3': 'numeric'})示例14: test_duplicate_column_names_with_whitespace
def test_duplicate_column_names_with_whitespace(self):
fp = get_data_path(
'invalid/duplicate-column-names-with-whitespace.tsv')
with self.assertRaisesRegex(MetadataFileError,
'Column names must be unique.*col1'):
Metadata.load(fp)示例15: test_column_types_unrecognized_column_name
def test_column_types_unrecognized_column_name(self):
fp = get_data_path('valid/simple.tsv')
with self.assertRaisesRegex(MetadataFileError,
'not_a_column.*column_types.*not a column '
'in the metadata file'):
Metadata.load(fp, column_types={'not_a_column': 'numeric'})