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src/c/o/cogent-1.5.3/cogent/seqsim/analysis.py   cogent(Download)
                  float64, max, min, average, any, pi
from cogent.util.array import without_diag
from cogent.maths.svd import three_item_combos, two_item_combos
from cogent.maths.stats.test import std
 
    leaves = list(tree.traverse())
    result = {}
    for first, second, third in three_item_combos(leaves):
        new_first, new_second, new_third = outgroup_last(first, second, third)
        #get the sequence from each node

src/p/y/pycogent-HEAD/cogent/seqsim/analysis.py   pycogent(Download)
                  float64, max, min, average, any, pi
from cogent.util.array import without_diag
from cogent.maths.svd import three_item_combos, two_item_combos
from cogent.maths.stats.test import std
 
    leaves = list(tree.traverse())
    result = {}
    for first, second, third in three_item_combos(leaves):
        new_first, new_second, new_third = outgroup_last(first, second, third)
        #get the sequence from each node

src/c/o/cogent-1.5.3/tests/test_maths/test_svd.py   cogent(Download)
#!/usr/bin/env python
"""Unit tests for the svd-supporting functionality."""
 
from cogent.util.unit_test import TestCase, main
from cogent.maths.svd import ratio_two_best, ratio_best_to_sum, \
    def test_three_item_combos(self):
        """three_item_combos should return items in correct order"""
        items = list(three_item_combos('abcde'))
        self.assertEqual(items, map(tuple, \
            ['abc','abd','abe','acd','ace','ade','bcd','bce','bde','cde']))

src/p/y/pycogent-HEAD/tests/test_maths/test_svd.py   pycogent(Download)
#!/usr/bin/env python
"""Unit tests for the svd-supporting functionality."""
 
from cogent.util.unit_test import TestCase, main
from cogent.maths.svd import ratio_two_best, ratio_best_to_sum, \
    def test_three_item_combos(self):
        """three_item_combos should return items in correct order"""
        items = list(three_item_combos('abcde'))
        self.assertEqual(items, map(tuple, \
            ['abc','abd','abe','acd','ace','ade','bcd','bce','bde','cde']))