本文整理汇总了Python中qiime.rarefaction.RarefactionMaker.rarefy_to_list方法的典型用法代码示例。如果您正苦于以下问题：Python RarefactionMaker.rarefy_to_list方法的具体用法？Python RarefactionMaker.rarefy_to_list怎么用？Python RarefactionMaker.rarefy_to_list使用的例子？那么, 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qiime.rarefaction.RarefactionMaker的用法示例。
在下文中一共展示了RarefactionMaker.rarefy_to_list方法的4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_rarefy_to_list
# 需要导入模块: from qiime.rarefaction import RarefactionMaker [as 别名]
# 或者: from qiime.rarefaction.RarefactionMaker import rarefy_to_list [as 别名]
def test_rarefy_to_list(self):
"""rarefy_to_list should rarefy correctly, same names, rm empty samples
"""
maker = RarefactionMaker(self.otu_tuple, 0, 1, 1, 1)
res = maker.rarefy_to_list(include_full=True)
self.assertFloatEqual(res[-1][2], self.sample_names)
self.assertFloatEqual(res[-1][3], self.taxon_names)
self.assertFloatEqual(res[-1][4], self.otu_table_transpose.T)
# each sample should have 1 seq, sample z should be removed
self.assertFloatEqual((res[1][4]).sum(0),[1.0,1.0] )示例2: test_rarefy_to_list
# 需要导入模块: from qiime.rarefaction import RarefactionMaker [as 别名]
# 或者: from qiime.rarefaction.RarefactionMaker import rarefy_to_list [as 别名]
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.assertFloatEqual(res[-1][2].SampleIds, self.otu_table.SampleIds)
self.assertFloatEqual(res[-1][2].ObservationIds, self.otu_table.ObservationIds)
self.assertEqual(res[-1][2], self.otu_table)
sample_value_sum = []
for val in res[1][2].iterSampleData():
sample_value_sum.append(val.sum())
self.assertFloatEqual(sample_value_sum, [1.0, 1.0])示例3: test_rarefy_to_list
# 需要导入模块: from qiime.rarefaction import RarefactionMaker [as 别名]
# 或者: from qiime.rarefaction.RarefactionMaker import rarefy_to_list [as 别名]
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])示例4: get_rarefactions
# 需要导入模块: from qiime.rarefaction import RarefactionMaker [as 别名]
# 或者: from qiime.rarefaction.RarefactionMaker import rarefy_to_list [as 别名]
def get_rarefactions(biom_object, minimum, maximum, iterations, steps):
"""rarify biom object and return rarefactions
Inputs:
biom_object: object to rarefy
minimum: starting point for the rarefactions
maximum: ending point for the rarefactions
iterations: repetitions per rarefaction depth
steps: number of levels between minimum and maximum
Outputs:
list of 3 element tuples, where each tuple contains as a 1st element the
rarefaction depth, as a 2nd element the iteration number and as a 3rd
element the rarefied biom corresponding to this depth
"""
rarefaction_step_size = int((maximum - minimum)/steps)
rarefaction_maker = RarefactionMaker(biom_object, minimum, maximum,\
rarefaction_step_size, iterations)
rarefactions = rarefaction_maker.rarefy_to_list()
return rarefactions