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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
 
    if average:
        #return symmetric matrix
        for first, second in two_item_combos(leaves):
            seq_1 = getattr(first, attr)
            seq_2 = getattr(second, attr)
            result[(first.Id, second.Id)] = \
                Counts.fromPair(seq_1, seq_2, alphabet)
    else:
        for first, second in two_item_combos(leaves):

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
 
    if average:
        #return symmetric matrix
        for first, second in two_item_combos(leaves):
            seq_1 = getattr(first, attr)
            seq_2 = getattr(second, attr)
            result[(first.Id, second.Id)] = \
                Counts.fromPair(seq_1, seq_2, alphabet)
    else:
        for first, second in two_item_combos(leaves):

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_two_item_combos(self):
        """two_item_combos should return items in correct order"""
        items = list(two_item_combos('abcd'))
        self.assertEqual(items, map(tuple, ['ab','ac','ad','bc','bd','cd']))
 

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_two_item_combos(self):
        """two_item_combos should return items in correct order"""
        items = list(two_item_combos('abcd'))
        self.assertEqual(items, map(tuple, ['ab','ac','ad','bc','bd','cd']))