def test_faith_pd_table_not_subset_tree(self):
tree = TreeNode.read(StringIO('((OTU1:0.5,OTU3:1.0):1.0)root;'))
table_ids = ['OTU1', 'OTU2']
table, tree = self.write_table_tree([1, 0], table_ids, ['foo'], tree)
expected_message = "The table does not appear to be completely "\
"represented by the phylogeny."
with self.assertRaisesRegex(ValueError, expected_message):
faith_pd(table, tree)
def faith_pd_work(self, u_counts, otu_ids, sample_ids, tree):
ta, tr = self.write_table_tree(u_counts, otu_ids, sample_ids, tree)
return faith_pd(ta, tr)
from unifrac import faith_pd
import time
import sys
print('Running-stacked_faith')
args = sys.argv
t0 = time.time()
obs = faith_pd(args[1], args[2])
t1 = time.time()
print('Python time-{}'.format(t1 - t0))
def faith_pd(table: BIOMV210Format, phylogeny: NewickFormat) -> pd.Series:
table_str = str(table)
tree_str = str(phylogeny)
result = unifrac.faith_pd(table_str, tree_str)
result.name = 'faith_pd'
return result
def transform(self, X):
with self.hdf5_table(X) as f:
fpd = faith_pd(f.name, self.tree_path)
return fpd.to_frame()