def test_call_phylogenetic(self):
"""AlphaDiversityCalc __call__ should call metric on phylo data
and return correct values"""
c = AlphaDiversityCalc(metric=PD_whole_tree, is_phylogenetic=True)
self.assertEqual(c(data_path=self.otu_table, tree_path=self.tree, \
taxon_names = self.otu_names, sample_names=self.sample_names),
[13, 17, 0])
def test_multi_return(self):
"""AlphaDiversityCalc __call__ should call metric on data
and return correct result for metric fn that returns a len 3 tuple
"""
c = AlphaDiversityCalc(osd)
res = c(data_path=self.otu_table1_fp)
assert_almost_equal(res, array([[2, 1, 1], [4, 4, 0], [0, 0, 0]]))
def single_object_alpha(biom_object, metrics, tree_object):
"""given a metric calculates alpha diversity of a biom object
Inputs:
biom_object: biom formatted OTU table
metrics: list of alpha diversity metrics
tree_object: tree object for the phylogenetic metrics
Output:
calculations: tab delimitted string with the calculations for the object
"""
calcs = []
for metric in metrics:
try:
metric_f = get_nonphylogenetic_metric(metric)
is_phylogenetic = False
except AttributeError:
try:
metric_f = get_phylogenetic_metric(metric)
is_phylogenetic = True
except AttributeError:
print 'something is wrong with conf file'
c = AlphaDiversityCalc(metric_f, is_phylogenetic)
calcs.append(c)
all_calcs = AlphaDiversityCalcs(calcs)
result = all_calcs(data_path=biom_object,
tree_path=tree_object,
log_path=None)
return all_calcs.formatResult(result)
def test_call_phylogenetic(self):
"""AlphaDiversityCalc __call__ should call metric on phylo data
and return correct values"""
c = AlphaDiversityCalc(metric=PD_whole_tree, is_phylogenetic=True)
assert_almost_equal(
c(data_path=self.otu_table1_fp,
tree_path=self.tree1,
taxon_names=self.otu_table1.ids(axis='observation'),
sample_names=self.otu_table1.ids()), [13, 17, 0])
def single_file_cup(otu_filepath, metrics, outfilepath, r, alpha, f, ci_type):
"""Compute variations of the conditional uncovered probability.
otufilepath: path to otu_table file
metrics: comma separated list of required metrics
outfilepath: path to output file
r: Number of new colors that are required for the next prediction
alpha: desired confidence level
f: ratio between upper and lower bound
ci_type: type of confidence interval. One of:
ULCL: upper and lower bounds with conservative lower bound
ULCU: upper and lower woth conservative upper bound
U: Upper bound only, lower bound fixed to 0
L: Lower bound only, upper bound fixed to 1
The opposite of uncovered probability is sometimes called coverage.
"""
metrics_list = metrics.split(',')
calcs = []
params = {'r': r,
'alpha': alpha,
'f':f,
'ci_type':ci_type}
for metric in metrics_list:
try:
metric_f = get_cup_metric(metric)
except AttributeError:
stderr.write(
"Could not find metric %s.\n Known metrics are: %s\n" \
% (metric, ', '.join(list_known_metrics())))
exit(1)
c = AlphaDiversityCalc(metric_f, params=params)
calcs.append(c)
all_calcs = AlphaDiversityCalcs(calcs)
try:
result = all_calcs(data_path=otu_filepath,
result_path=outfilepath, log_path=None)
if result: #can send to stdout instead of file
print all_calcs.formatResult(result)
except IOError, e:
stderr.write("Failed because of missing files.\n")
stderr.write(str(e)+'\n')
exit(1)
def test_call_phylogenetic_escaped_names(self):
"""AlphaDiversityCalc __call__ should call metric on phylo data
and return correct values"""
c = AlphaDiversityCalc(metric=PD_whole_tree, is_phylogenetic=True)
expected = [13, 17, 0]
non_escaped_result = c(data_path=self.otu_table, tree_path=self.tree, \
taxon_names = self.otu_names, sample_names=self.sample_names)
otu_table = array([[2, 0, 0, 1], [1, 1, 1, 1], [0, 0, 0, 0]])
sample_names = list('XYZ')
otu_names = ['a', 'b', 'c', 'd_']
tree_str = "((a:2,'b':3):2,(c:1,'d_':2):7);"
tree_fp = get_tmp_filename(prefix='Alpha_div_tests', suffix='.tre')
open(tree_fp, 'w').write(tree_str)
self.files_to_remove.append(tree_fp)
escaped_result = c(data_path=otu_table, tree_path=tree_fp, \
taxon_names = otu_names, sample_names=sample_names)
self.assertEqual(non_escaped_result, escaped_result)
def test_call_phylogenetic_escaped_names(self):
"""AlphaDiversityCalc __call__ should call metric on phylo data
and return correct values"""
c = AlphaDiversityCalc(metric=PD_whole_tree, is_phylogenetic=True)
expected = [13., 17., 0.]
non_escaped_result = c(data_path=self.otu_table1_fp,
tree_path=self.tree1,
taxon_names=self.otu_table1.ObservationIds,
sample_names=self.otu_table1.SampleIds)
escaped_result = c(data_path=self.otu_table2_fp,
tree_path=self.tree2,
taxon_names=self.otu_table2.ObservationIds,
sample_names=self.otu_table2.SampleIds)
self.assertEqual(non_escaped_result, expected)
self.assertEqual(escaped_result, expected)
self.assertEqual(non_escaped_result, escaped_result)
def test_1sample(self):
""" should work if only testing one sample as well"""
c = AlphaDiversityCalc(observed_otus)
self.assertEqual(c(data_path=self.single_sample_otu_table_fp), [2])
def test_call(self):
"""AlphaDiversityCalc __call__ should call metric on data
and return correct result"""
c = AlphaDiversityCalc(observed_otus)
assert_almost_equal(c(data_path=self.otu_table1_fp), [2, 4, 0])
def test_init(self):
"""AlphaDiversity __init__ should store metric, name, params"""
c = AlphaDiversityCalc(observed_otus)
self.assertEqual(c.Metric, observed_otus)
self.assertEqual(c.Params, {})
def test_1sample(self):
""" should work if only testing one sample as well"""
otu_table = array([[2, 0, 0, 1]])
c = AlphaDiversityCalc(alph454.alph.observed_species)
self.assertEqual(c(data_path=otu_table), [2])
def test_call(self):
"""AlphaDiversityCalc __call__ should call metric on data
and return correct result"""
c = AlphaDiversityCalc(observed_species)
self.assertEqual(c(data_path=self.otu_table), [2, 4, 0])
