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Util #12

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merged 13 commits into from
Jul 26, 2016
Merged

Util #12

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362fe9e
ENH: Adding util functions
mortonjt Jul 19, 2016
a1b9cef
STY: pep8
mortonjt Jul 19, 2016
2908c93
STY: Flake8 to the rescue
mortonjt Jul 19, 2016
e2e2e63
STY: Addressing @antgonza and @josenavas comments
mortonjt Jul 19, 2016
d6a037b
STY: pep8 flake8
mortonjt Jul 19, 2016
d197605
DOC: Changing method name
mortonjt Jul 19, 2016
2ded931
STY: clean up pep8/flake8
mortonjt Jul 19, 2016
a54d051
Merge branch 'master' of https://github.com/biocore/gneiss into util
mortonjt Jul 20, 2016
477d196
DOC: Updating changelog
mortonjt Jul 20, 2016
371cc16
ENH: Adding inplace option
mortonjt Jul 25, 2016
6d70cf9
STY: Code dereplication
mortonjt Jul 26, 2016
9003db8
DOC: cleaning up docstrings
mortonjt Jul 26, 2016
b049ced
pep8
mortonjt Jul 26, 2016
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,7 @@
## Version 0.0.2 (changes since 0.0.2 go here)

### Features
* Adding in utility functions for handing feature tables, metadata, and trees. [#12](https://github.com/biocore/gneiss/pull/12)
* Adding GPL license.

### Bug fixes
322 changes: 322 additions & 0 deletions gneiss/tests/test_util.py
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@@ -0,0 +1,322 @@
# ----------------------------------------------------------------------------
# Copyright (c) 2016--, gneiss development team.
#
# Distributed under the terms of the GPLv3 License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------

import unittest
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I realized that none of this files have the copyright notice on top. Should it be added?

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👍

import pandas as pd
import pandas.util.testing as pdt
from skbio import TreeNode
from gneiss.util import match, match_tips, rename_internal_nodes


class TestUtil(unittest.TestCase):

def test_match(self):
table = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['o1', 'o2', 'o3', 'o4'])
metadata = pd.DataFrame([['a', 'control'],
['b', 'control'],
['c', 'diseased'],
['d', 'diseased']],
index=['s1', 's2', 's3', 's4'],
columns=['Barcode', 'Treatment'])
exp_table, exp_metadata = table, metadata
res_table, res_metadata = match(table, metadata)
pdt.assert_frame_equal(exp_table, res_table)
pdt.assert_frame_equal(exp_metadata, res_metadata)

def test_match_immutable(self):
# tests to make sure that the original tables don't change.
table = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['o1', 'o2', 'o3', 'o4'])
metadata = pd.DataFrame([['a', 'control'],
['c', 'diseased'],
['b', 'control']],
index=['s1', 's3', 's2'],
columns=['Barcode', 'Treatment'])

exp_table = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['o1', 'o2', 'o3', 'o4'])
exp_metadata = pd.DataFrame([['a', 'control'],
['c', 'diseased'],
['b', 'control']],
index=['s1', 's3', 's2'],
columns=['Barcode', 'Treatment'])
match(table, metadata, intersect=True)
pdt.assert_frame_equal(table, exp_table)
pdt.assert_frame_equal(metadata, exp_metadata)

def test_match_duplicate(self):
table1 = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s2', 's2', 's3', 's4'],
columns=['o1', 'o2', 'o3', 'o4'])
metadata1 = pd.DataFrame([['a', 'control'],
['b', 'control'],
['c', 'diseased'],
['d', 'diseased']],
index=['s1', 's2', 's3', 's4'],
columns=['Barcode', 'Treatment'])

table2 = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['o1', 'o2', 'o3', 'o4'])
metadata2 = pd.DataFrame([['a', 'control'],
['b', 'control'],
['c', 'diseased'],
['d', 'diseased']],
index=['s1', 's1', 's3', 's4'],
columns=['Barcode', 'Treatment'])

with self.assertRaises(ValueError):
match(table1, metadata1)
with self.assertRaises(ValueError):
match(table2, metadata2)

def test_match_scrambled(self):
table = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['o1', 'o2', 'o3', 'o4'])
metadata = pd.DataFrame([['a', 'control'],
['c', 'diseased'],
['b', 'control'],
['d', 'diseased']],
index=['s1', 's3', 's2', 's4'],
columns=['Barcode', 'Treatment'])
exp_table = table
exp_metadata = pd.DataFrame([['a', 'control'],
['b', 'control'],
['c', 'diseased'],
['d', 'diseased']],
index=['s1', 's2', 's3', 's4'],
columns=['Barcode', 'Treatment'])

res_table, res_metadata = match(table, metadata)
pdt.assert_frame_equal(exp_table, res_table)
pdt.assert_frame_equal(exp_metadata, res_metadata)

def test_match_intersect(self):
table = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['o1', 'o2', 'o3', 'o4'])
metadata = pd.DataFrame([['a', 'control'],
['c', 'diseased'],
['b', 'control']],
index=['s1', 's3', 's2'],
columns=['Barcode', 'Treatment'])

exp_table = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3]],
index=['s1', 's2', 's3'],
columns=['o1', 'o2', 'o3', 'o4'])

exp_metadata = pd.DataFrame([['a', 'control'],
['b', 'control'],
['c', 'diseased']],
index=['s1', 's2', 's3'],
columns=['Barcode', 'Treatment'])

res_table, res_metadata = match(table, metadata, intersect=True)
pdt.assert_frame_equal(exp_table, res_table)
pdt.assert_frame_equal(exp_metadata, res_metadata)

def test_match_mismatch(self):
table = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['o1', 'o2', 'o3', 'o4'])
metadata = pd.DataFrame([['a', 'control'],
['c', 'diseased'],
['b', 'control']],
index=['s1', 's3', 's2'],
columns=['Barcode', 'Treatment'])
with self.assertRaises(ValueError):
match(table, metadata)

def test_match_tips(self):
table = pd.DataFrame([[0, 0, 1, 1],
[2, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'c', 'd'])
tree = TreeNode.read([u"(((a,b)f, c),d)r;"])
exp_table, exp_tree = table, tree
res_table, res_tree = match_tips(table, tree)
pdt.assert_frame_equal(exp_table, res_table)
self.assertEqual(str(exp_tree), str(res_tree))

def test_match_tips_scrambled_tips(self):
table = pd.DataFrame([[0, 0, 1, 1],
[2, 3, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'c', 'd'])
tree = TreeNode.read([u"(((b,a)f, c),d)r;"])
exp_tree = tree
exp_table = pd.DataFrame([[0, 0, 1, 1],
[3, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['b', 'a', 'c', 'd'])

res_table, res_tree = match_tips(table, tree)
pdt.assert_frame_equal(exp_table, res_table)
self.assertEqual(str(exp_tree), str(res_tree))

def test_match_tips_scrambled_columns(self):
table = pd.DataFrame([[0, 0, 1, 1],
[3, 2, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['b', 'a', 'c', 'd'])
tree = TreeNode.read([u"(((a,b)f, c),d)r;"])
exp_tree = tree
exp_table = pd.DataFrame([[0, 0, 1, 1],
[2, 3, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'c', 'd'])

res_table, res_tree = match_tips(table, tree)
pdt.assert_frame_equal(exp_table, res_table)
self.assertEqual(str(exp_tree), str(res_tree))

def test_match_tips_intersect_tips(self):
# there are less tree tips than table columns
table = pd.DataFrame([[0, 0, 1, 1],
[2, 3, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'c', 'd'])
tree = TreeNode.read([u"((a,b)f,d)r;"])
exp_table = pd.DataFrame([[0, 0, 1],
[2, 3, 4],
[5, 5, 3],
[0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'd'])
exp_tree = tree
res_table, res_tree = match_tips(table, tree, intersect=True)
pdt.assert_frame_equal(exp_table, res_table)
self.assertEqual(str(exp_tree), str(res_tree))

def test_match_tips_intersect_columns(self):
# table has less columns than tree tips
table = pd.DataFrame([[0, 0, 1],
[2, 3, 4],
[5, 5, 3],
[0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'd'])
tree = TreeNode.read([u"(((a,b)f, c),d)r;"])
exp_table = pd.DataFrame([[1, 0, 0],
[4, 2, 3],
[3, 5, 5],
[1, 0, 0]],
index=['s1', 's2', 's3', 's4'],
columns=['d', 'a', 'b'])
exp_tree = TreeNode.read([u"(d,(a,b)f)r;"])
res_table, res_tree = match_tips(table, tree, intersect=True)
pdt.assert_frame_equal(exp_table, res_table)
self.assertEqual(str(exp_tree), str(res_tree))

def test_match_tips_intersect_tree_immutable(self):
# tests to see if tree chnages.
table = pd.DataFrame([[0, 0, 1],
[2, 3, 4],
[5, 5, 3],
[0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'd'])
tree = TreeNode.read([u"(((a,b)f, c),d)r;"])
match_tips(table, tree, intersect=True)
self.assertEqual(str(tree), u"(((a,b)f,c),d)r;\n")

def test_match_tips_mismatch(self):
# table has less columns than tree tips
table = pd.DataFrame([[0, 0, 1],
[2, 3, 4],
[5, 5, 3],
[0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'd'])
tree = TreeNode.read([u"(((a,b)f, c),d)r;"])
with self.assertRaises(ValueError):
match_tips(table, tree)

table = pd.DataFrame([[0, 0, 1, 1],
[2, 3, 4, 4],
[5, 5, 3, 3],
[0, 0, 0, 1]],
index=['s1', 's2', 's3', 's4'],
columns=['a', 'b', 'c', 'd'])
tree = TreeNode.read([u"((a,b)f,d)r;"])
with self.assertRaises(ValueError):
match_tips(table, tree)

def test_rename_internal_nodes(self):
tree = TreeNode.read([u"(((a,b), c),d)r;"])
exp_tree = TreeNode.read([u"(((a,b)y2, c)y1,d)y0;"])
res_tree = rename_internal_nodes(tree)
self.assertEqual(str(exp_tree), str(res_tree))

def test_rename_internal_nodes_names(self):
tree = TreeNode.read([u"(((a,b), c),d)r;"])
exp_tree = TreeNode.read([u"(((a,b)ab, c)abc,d)r;"])
res_tree = rename_internal_nodes(tree, ['r', 'abc', 'ab'])
self.assertEqual(str(exp_tree), str(res_tree))

def test_rename_internal_nodes_names_mismatch(self):
tree = TreeNode.read([u"(((a,b), c),d)r;"])
with self.assertRaises(ValueError):
rename_internal_nodes(tree, ['r', 'abc'])

def test_rename_internal_nodes_warning(self):
tree = TreeNode.read([u"(((a,b)y2, c),d)r;"])
with self.assertWarns(Warning):
rename_internal_nodes(tree)

def test_rename_internal_nodes_immutable(self):
tree = TreeNode.read([u"(((a,b)y2, c),d)r;"])
rename_internal_nodes(tree)
self.assertEqual(str(tree), "(((a,b)y2,c),d)r;\n")


if __name__ == '__main__':
unittest.main()
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