本文整理汇总了Python中biom.table.Table.norm方法的典型用法代码示例。如果您正苦于以下问题：Python Table.norm方法的具体用法？Python Table.norm怎么用？Python Table.norm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.norm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: TopLevelTests
# 需要导入模块: from biom.table import Table [as 别名]
# 或者: from biom.table.Table import norm [as 别名]
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
self.otu_table_vals = array([[1, 0, 2, 4],
[1, 2, 0, 1],
[0, 1, 1, 0],
[1, 2, 1, 0]])
self.otu_table = Table(self.otu_table_vals,
['0', '1', '2', '3'],
['s1', 's2', 's3', 's4'],
[{"taxonomy": ["Root", "Bacteria", "Actinobacteria", "Actinobacteria", "Coriobacteridae", "Coriobacteriales", "Coriobacterineae", "Coriobacteriaceae"]},
{"taxonomy": ["Root",
"Bacteria",
"Firmicutes",
"\"Clostridia\""]},
{"taxonomy": ["Root",
"Bacteria",
"Firmicutes",
"\"Clostridia\""]},
{"taxonomy": ["Root", "Bacteria"]}],
None,)
self.mapping = """#SampleID\tBarcodeSequence\tTreatment\tDescription
#Test mapping file
s1\tAAAA\tControl\tControl mouse, I.D. 354
s2\tGGGG\tControl\tControl mouse, I.D. 355
s3\tCCCC\tExp\tDisease mouse, I.D. 356
s4\tTTTT\tExp\tDisease mouse, I.D. 357""".split('\n')
def test_sum_counts_by_consensus(self):
"""should sum otu counts by consensus"""
#otu_table = parse_otu_table(self.otu_table)
#otu_table = parse_biom_table(self.otu_table)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 3)
exp_result = {(
'Root', 'Bacteria', 'Actinobacteria'): array([1, 0, 2, 4]),
('Root', 'Bacteria', 'Firmicutes'): array([1, 3, 1, 1]),
('Root', 'Bacteria', 'Other'): array([1, 2, 1, 0])}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertItemsEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 2)
exp_result = {('Root', 'Bacteria'): array([3, 5, 4, 5])}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertItemsEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
obs_result, obs_mapping = sum_counts_by_consensus(self.otu_table, 4)
exp_result = {('Root', 'Bacteria', 'Actinobacteria', 'Actinobacteria'):
array([1, 0, 2, 4]),
('Root', 'Bacteria', 'Firmicutes', '"Clostridia"'):
array([1, 3, 1, 1]),
('Root', 'Bacteria', 'Other', 'Other'): array([1, 2, 1, 0])}
exp_mapping = {'s1': 0, 's2': 1, 's3': 2, 's4': 3}
self.assertItemsEqual(obs_result, exp_result)
self.assertEqual(obs_mapping, exp_mapping)
def test_make_new_summary_file(self):
"""make_new_summary_file works
"""
lower_percentage, upper_percentage = None, None
#otu_table = parse_otu_table(self.otu_table, int)
#otu_table = parse_biom_table(self.otu_table)
summary, header = make_summary(
self.otu_table, 3, upper_percentage, lower_percentage)
self.assertEqual(header, ['Taxon', 's1', 's2', 's3', 's4'])
self.assertEqual(
summary, [[('Root', 'Bacteria', 'Actinobacteria'), 1, 0, 2, 4],
[('Root', 'Bacteria', 'Firmicutes'),
1, 3, 1, 1],
[('Root', 'Bacteria', 'Other'), 1, 2, 1, 0]])
# test that works with relative abundances
#otu_table = parse_otu_table(self.otu_table, float)
#otu_table = parse_biom_table(self.otu_table, float)
#otu_table = convert_otu_table_relative(otu_table)
otu_table = self.otu_table.norm(axis='sample', inplace=False)
summary, header = make_summary(
otu_table, 3, upper_percentage, lower_percentage)
self.assertEqual(header, ['Taxon', 's1', 's2', 's3', 's4'])
self.assertEqual(summary[0][0], ('Root', 'Bacteria', 'Actinobacteria'))
assert_almost_equal(summary[0][1:], [1.0 / 3, 0.0, 0.5, 0.8])
self.assertEqual(summary[1][0], ('Root', 'Bacteria', 'Firmicutes'))
assert_almost_equal(summary[1][1:], [1.0 / 3, 0.6, 0.25, 0.2])
self.assertEqual(summary[2][0], ('Root', 'Bacteria', 'Other'))
assert_almost_equal(summary[2][1:], [1.0 / 3, 0.4, 0.25, 0.0])
##
# testing lower triming
lower_percentage, upper_percentage = 0.3, None
summary, header = make_summary(
otu_table, 3, upper_percentage, lower_percentage)
self.assertEqual(summary[0][0], ('Root', 'Bacteria', 'Other'))
assert_almost_equal(summary[0][1:], [1.0 / 3, 0.4, 0.25, 0.0])
##
#.........这里部分代码省略.........