本文整理汇总了Python中biom.table.Table.get_value_by_ids方法的典型用法代码示例。如果您正苦于以下问题：Python Table.get_value_by_ids方法的具体用法？Python Table.get_value_by_ids怎么用？Python Table.get_value_by_ids使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类biom.table.Table的用法示例。
在下文中一共展示了Table.get_value_by_ids方法的1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: FunctionTests
# 需要导入模块: from biom.table import Table [as 别名]
# 或者: from biom.table.Table import get_value_by_ids [as 别名]
#.........这里部分代码省略.........
prefix='test_rarefaction_dir', suffix='')
write_biom_table(self.otu_table, self.otu_table_fp)
write_biom_table(self.otu_table_meta, self.otu_table_meta_fp)
self._paths_to_clean_up = [self.otu_table_fp, self.otu_table_meta_fp]
self._dirs_to_clean_up = [self.rare_dir]
def tearDown(self):
""" cleanup temporary files """
map(remove, self._paths_to_clean_up)
for d in self._dirs_to_clean_up:
if os.path.exists(d):
rmtree(d)
def test_rarefy_to_list(self):
"""rarefy_to_list should rarefy correctly, same names
"""
maker = RarefactionMaker(self.otu_table_fp, 0, 1, 1, 1)
res = maker.rarefy_to_list(include_full=True)
self.assertItemsEqual(res[-1][2].ids(), self.otu_table.ids())
self.assertItemsEqual(
res[-1][2].ids(axis='observation'),
self.otu_table.ids(axis='observation'))
self.assertEqual(res[-1][2], self.otu_table)
sample_value_sum = []
for val in res[1][2].iter_data(axis='sample'):
sample_value_sum.append(val.sum())
npt.assert_almost_equal(sample_value_sum, [1.0, 1.0])
def test_rarefy_to_files(self):
"""rarefy_to_files should write valid files
"""
maker = RarefactionMaker(self.otu_table_fp, 1, 2, 1, 1)
maker.rarefy_to_files(
self.rare_dir,
include_full=True,
include_lineages=False)
fname = os.path.join(self.rare_dir, "rarefaction_1_0.biom")
otu_table = load_table(fname)
self.assertItemsEqual(
otu_table.ids(),
self.otu_table.ids()[:2])
# third sample had 0 seqs, so it's gone
def test_rarefy_to_files2(self):
"""rarefy_to_files should write valid files with some metadata on otus
"""
maker = RarefactionMaker(self.otu_table_meta_fp, 1, 2, 1, 1)
maker.rarefy_to_files(
self.rare_dir,
include_full=True,
include_lineages=False)
fname = os.path.join(self.rare_dir, "rarefaction_1_0.biom")
otu_table = load_table(fname)
self.assertItemsEqual(
otu_table.ids(),
self.otu_table.ids()[:2])
# third sample had 0 seqs, so it's gone
def test_get_empty_rare(self):
"""get_rare_data should be empty when depth > # seqs in any sample"""
self.assertRaises(TableException, get_rare_data, self.otu_table,
50, include_small_samples=False)
def test_get_overfull_rare(self):
"""get_rare_data should be identical to given in this case
here, rare depth > any sample, and include_small... = True"""
rare_otu_table = get_rare_data(self.otu_table,
50, include_small_samples=True)
self.assertEqual(len(rare_otu_table.ids()), 3)
# 4 observations times 3 samples = size 12 before
self.assertEqual(len(rare_otu_table.ids(axis='observation')), 4)
for sam in self.otu_table.ids():
for otu in self.otu_table.ids(axis='observation'):
rare_val = rare_otu_table.get_value_by_ids(otu, sam)
self.assertEqual(rare_otu_table.get_value_by_ids(otu, sam),
self.otu_table.get_value_by_ids(otu, sam))
def test_get_11depth_rare(self):
"""get_rare_data should get only sample X
"""
rare_otu_table = get_rare_data(self.otu_table,
11, include_small_samples=False)
self.assertEqual(rare_otu_table.ids(), ('X',))
# a very complicated way to test things
rare_values = [val[0]
for (val, otu_id, meta) in rare_otu_table.iter(axis='observation')]
self.assertEqual(rare_values, [1.0, 5.0, 3.0, 2.0])