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test_sort.py
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test_sort.py
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#!/usr/bin/env python
# File created on 15 Feb 2011
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Yoshiki Vazquez Baeza"]
__license__ = "GPL"
__version__ = "1.6.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import remove_files
from qiime.parse import parse_mapping_file
from biom.parse import parse_biom_table_str
from qiime.sort import (sort_sample_ids_by_mapping_value,
sort_fasta_by_abundance, natsort,
natsort_case_insensitive, sort_otu_table,
sort_otu_table_by_mapping_field, signed_natsort)
class SortTests(TestCase):
def setUp(self):
self.mapping_f1 = mapping_f1.split('\n')
self.otu_table1 = otu_table1
self.mapping_f2 = mapping_f2.split('\n')
self.age_sorted_otu_table1 = age_sorted_otu_table1
self.name_sorted_otu_table1 = name_sorted_otu_table1
self.nothing_sorted_otu_table1 = nothing_sorted_otu_table1
self.otu_table1_bad_sampleID = otu_table1_bad_sampleID
self.dirs_to_remove = []
self.files_to_remove = []
def tearDown(self):
for dir in self.dirs_to_remove:
if exists(dir):
rmdir(dir)
remove_files(self.files_to_remove)
def test_sort_sample_ids_by_mapping_value(self):
""" sort_sample_ids_by_mapping_value functions as expected """
actual = sort_sample_ids_by_mapping_value(mapping_file=self.mapping_f1,
field='days_since_epoch',
field_type_f=float)
expected = zip(['NotInOtuTable','1','Z2','Z1','A'],
[0.0,5.7,10,23,400000])
self.assertEqual(actual,expected)
def test_sort_sample_ids_by_mapping_value_error(self):
""" sort_sample_ids_by_mapping_value handles errors """
self.assertRaises(ValueError,
sort_sample_ids_by_mapping_value,
mapping_file=self.mapping_f1,
field='years_since_spoch',
field_type_f=float)
self.assertRaises(ValueError,
sort_sample_ids_by_mapping_value,
mapping_file=self.mapping_f1,
field='Something',
field_type_f=float)
def test_sort_fasta_by_abundance(self):
"""sort_fasta_by_abundance functions as expected"""
class FakeOutF(object):
def __init__(self):
self.s = ""
def write(self,s):
self.s += s
actual = FakeOutF()
expected = ""
sort_fasta_by_abundance([],actual)
self.assertEqual(actual.s,expected)
# no sorting necessary
actual = FakeOutF()
expected1 = "\n".join(['>s1','ACCGT','>s2 comment','ATTGC',''])
expected2 = "\n".join(['>s2 comment','ATTGC','>s1','ACCGT',''])
sort_fasta_by_abundance(['>s1','ACCGT','>s2 comment','ATTGC'],actual)
# order is unimportant here
self.assertTrue(actual.s == expected1 or actual.s == expected2)
# sorting necessary
actual = FakeOutF()
inseqs = ['>s1','ACCGT',
'>s2 comment','ATTGC',
'>s3 blah','ATTGC']
expected = "\n".join(['>s2 comment','ATTGC',
'>s3 blah','ATTGC',
'>s1','ACCGT',''])
sort_fasta_by_abundance(inseqs,actual)
self.assertEqual(actual.s,expected)
def test_natsort(self):
"""natsort should perform numeric comparisons on strings"""
# string with alpha and numerics sort correctly
s = 'sample1 sample2 sample11 sample12'.split()
self.assertEqual(natsort(s),
'sample1 sample2 sample11 sample12'.split())
s.reverse()
self.assertEqual(natsort(s),
'sample1 sample2 sample11 sample12'.split())
self.assertEqual(natsort(list('cba321')),list('123abc'))
# strings with alpha only sort correctly
self.assertEqual(natsort(list('cdba')),list('abcd'))
# string of ints sort correctly
self.assertEqual(natsort(['11','2','1','0']),
['0','1','2','11'])
# strings of floats sort correctly
self.assertEqual(natsort(['1.11','1.12','1.00','0.009']),
['0.009','1.00','1.11','1.12'])
# string of ints sort correctly
self.assertEqual(natsort([('11','A'),('2','B'),('1','C'),('0','D')]),
[('0','D'),('1','C'),('2','B'),('11','A')])
#
def test_natsort_case_insensitive(self):
"""natsort should perform numeric comparisons on strings and is
_not_ case-sensitive"""
# string with alpha and numerics sort correctly
s = ['sample1', 'sample2', 'sample11', 'sample12', 'SAmple1', 'Sample2']
# expected values
exp_natsort=['SAmple1','Sample2', 'sample1', 'sample2', 'sample11',
'sample12']
exp_natsort_case_insensitive=['sample1','SAmple1','sample2',
'Sample2','sample11', 'sample12']
# test natsort
self.assertEqual(natsort(s),exp_natsort)
# test natsort_case_insensitive
self.assertEqual(natsort_case_insensitive(s),
exp_natsort_case_insensitive)
s.reverse()
# test natsort
self.assertEqual(natsort(s), exp_natsort)
# test natsort_case_insensitive
self.assertEqual(natsort(list('cbaA321')),list('123Aabc'))
# strings with alpha only sort correctly
self.assertEqual(natsort_case_insensitive(list('cdBa')),list('aBcd'))
# string of ints sort correctly
self.assertEqual(natsort_case_insensitive(['11','2','1','0']),
['0','1','2','11'])
# strings of floats sort correctly
self.assertEqual(natsort_case_insensitive(['1.11','1.12','1.00',
'0.009']),['0.009','1.00',
'1.11','1.12'])
# string of ints sort correctly
self.assertEqual(natsort_case_insensitive([('11','A'),('2','B'),
('1','C'),('0','D')]),
[('0','D'),('1','C'),
('2','B'),('11','A')])
def test_sort_otu_table_by_mapping_field_all_values_differ(self):
""" sort_otu_table_by_mapping_field fns when all values differ"""
actual = sort_otu_table_by_mapping_field(parse_biom_table_str(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Age")
expected = parse_biom_table_str(self.age_sorted_otu_table1)
self.assertEqual(actual, expected)
def test_sort_otu_table(self):
""" sort_otu_table fns as expected """
actual = sort_otu_table(parse_biom_table_str(self.otu_table1),
['NA','Key','Fing'])
expected = parse_biom_table_str(self.age_sorted_otu_table1)
self.assertEqual(actual, expected)
def test_sort_otu_table_error(self):
""" sort_otu_table handles errors """
self.assertRaises(ValueError,sort_otu_table,
parse_biom_table_str(self.otu_table1),['NA','Key','Fing','Key'])
self.assertRaises(KeyError,sort_otu_table,
parse_biom_table_str(self.otu_table1),['NA','Key'])
def test_sort_otu_table_by_mapping_field_some_values_differ(self):
""" sort_otu_table fns when some values differ"""
actual = sort_otu_table_by_mapping_field(parse_biom_table_str(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Nothing")
expected = parse_biom_table_str(self.nothing_sorted_otu_table1)
self.assertEqual(actual, expected)
def test_sort_otu_table_by_mapping_field_some_values_same(self):
""" sort_otu_table_by_mapping_field fns when all values are the same"""
actual = sort_otu_table_by_mapping_field(parse_biom_table_str(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Name")
expected = parse_biom_table_str(self.name_sorted_otu_table1)
self.assertEqual(actual, expected)
def test_sort_otu_table_by_mapping_field_error(self):
""" sort_otu_table_by_mapping_field fails on samples in otu table but not mapping"""
self.assertRaises(KeyError,sort_otu_table_by_mapping_field,
parse_biom_table_str(self.otu_table1_bad_sampleID),
parse_mapping_file(self.mapping_f2),
sort_field = "Age")
def test_signed_sort(self):
"""Test correct sorting of different data types"""
# an empty list must be returned when an empty list needs to be sorted
self.assertEqual(signed_natsort([]), [])
# tuples that can be sorted by type-casting the first element
test_list = [('9', 'SampleA'), ('-1', 'SampleD'), ('7', 'SampleC'),
('-2', 'SampleE'), ('-0.11', 'SampleF'), ('17.11', 'SampleB'),
('100', 'SampleG'), ('13', 'SampleH')]
expected_result = [('-2', 'SampleE'), ('-1', 'SampleD'),
('-0.11', 'SampleF'), ('7', 'SampleC'), ('9', 'SampleA'),
('13', 'SampleH'), ('17.11', 'SampleB'), ('100', 'SampleG')]
output = signed_natsort(test_list)
self.assertEquals(output, expected_result)
# tuples that must be sorted alphabetically
test_list = [('Cygnus', 'SampleA'), ('Cepheus', 'SampleD'),
('Auriga', 'SampleC'), ('Grus', 'SampleE'), ('Hydra', 'SampleF'),
('Carina', 'SampleB'), ('Orion', 'SampleG'), ('Lynx', 'SampleH')]
expected_result = [('Auriga', 'SampleC'), ('Carina', 'SampleB'),
('Cepheus', 'SampleD'), ('Cygnus', 'SampleA'), ('Grus', 'SampleE'),
('Hydra', 'SampleF'), ('Lynx', 'SampleH'), ('Orion', 'SampleG')]
output = signed_natsort(test_list)
self.assertEquals(output, expected_result)
# mixed case, tuples will be sorted alpha-numerically
test_list = [('Cygnus', 'SampleA'), ('Cepheus', 'SampleD'),
('Auriga', 'SampleC'), ('Grus', 'SampleE'), ('-0.11', 'SampleF'),
('17.11', 'SampleB'), ('100', 'SampleG'), ('Lynx', 'SampleH')]
expected_result = [('17.11', 'SampleB'), ('100', 'SampleG'),
('-0.11', 'SampleF'), ('Auriga', 'SampleC'), ('Cepheus', 'SampleD'),
('Cygnus', 'SampleA'), ('Grus', 'SampleE'), ('Lynx', 'SampleH')]
output = signed_natsort(test_list)
self.assertEquals(output, expected_result)
# mixed case just a list
test_list = ['foo', 'bar', '-100', '12', 'spam', '4', '-1']
expected_result = ['4', '12', '-1', '-100', 'bar', 'foo', 'spam']
output = signed_natsort(test_list)
self.assertEquals(output, expected_result)
# list of elements that can be type-casted
test_list = ['0', '1', '14', '12', '-15', '4', '-1']
expected_result = ['-15', '-1', '0', '1', '4', '12', '14']
output = signed_natsort(test_list)
self.assertEquals(output, expected_result)
# mixed dict case
test_dict = {'foo':'a', 'bar':'b', '-100':'1', '12':'11', 'spam':'q',
'4':'11', '-1':'e'}
expected_result = ['4', '12', '-1', '-100', 'bar', 'foo', 'spam']
output = signed_natsort(test_dict)
self.assertEquals(output, expected_result)
# dict where the keys can be type-casted
test_dict = {'0':'foo', '1':'bar', '14':'stand', '12':'eggs', '-15':'q',
'4':'b', '-1':'h'}
expected_result = ['-15', '-1', '0', '1', '4', '12', '14']
output = signed_natsort(test_dict)
self.assertEquals(output, expected_result)
mapping_f1 = """#SampleID\tSomething\tdays_since_epoch
Z1\t42\t23
Z2\thello\t10
A\t4\t400000
1\tr\t5.7
NotInOtuTable\tf\t0"""
otu_table1 = '{"rows": [{"id": "0", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Propionibacterineae", "Propionibacterium"]}}, {"id": "1", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Lactobacillales", "Lactobacillales", "Streptococcaceae", "Streptococcus"]}}, {"id": "2", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Gordoniaceae", "Corynebacteriaceae"]}}, {"id": "3", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Staphylococcaceae"]}}, {"id": "4", "metadata": {"taxonomy": ["Bacteria", "Cyanobacteria", "Chloroplasts", "vectors"]}}], "format": "Biological Observation Matrix v0.9", "data": [[0, 0, 19111.0], [0, 1, 44536.0], [0, 2, 42.0], [1, 0, 1216.0], [1, 1, 3500.0], [1, 2, 6.0], [2, 0, 1803.0], [2, 1, 1184.0], [2, 2, 2.0], [3, 0, 1722.0], [3, 1, 4903.0], [3, 2, 17.0], [4, 0, 589.0], [4, 1, 2074.0], [4, 2, 34.0]], "columns": [{"id": "Fing", "metadata": null}, {"id": "Key", "metadata": null}, {"id": "NA", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2572", "matrix_type": "sparse", "shape": [5, 3], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2011-12-21T20:26:01.408138", "type": "OTU table", "id": null, "matrix_element_type": "float"}'
otu_table1_bad_sampleID = '{"rows": [{"id": "0", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Propionibacterineae", "Propionibacterium"]}}, {"id": "1", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Lactobacillales", "Lactobacillales", "Streptococcaceae", "Streptococcus"]}}, {"id": "2", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Gordoniaceae", "Corynebacteriaceae"]}}, {"id": "3", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Staphylococcaceae"]}}, {"id": "4", "metadata": {"taxonomy": ["Bacteria", "Cyanobacteria", "Chloroplasts", "vectors"]}}], "format": "Biological Observation Matrix v0.9", "data": [[0, 0, 19111.0], [0, 1, 44536.0], [0, 2, 42.0], [1, 0, 1216.0], [1, 1, 3500.0], [1, 2, 6.0], [2, 0, 1803.0], [2, 1, 1184.0], [2, 2, 2.0], [3, 0, 1722.0], [3, 1, 4903.0], [3, 2, 17.0], [4, 0, 589.0], [4, 1, 2074.0], [4, 2, 34.0]], "columns": [{"id": "Fing", "metadata": null}, {"id": "Key", "metadata": null}, {"id": "NotInMapping", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2572", "matrix_type": "sparse", "shape": [5, 3], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2011-12-21T20:19:02.153603", "type": "OTU table", "id": null, "matrix_element_type": "float"}'
age_sorted_otu_table1 = '{"rows": [{"id": "0", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Propionibacterineae", "Propionibacterium"]}}, {"id": "1", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Lactobacillales", "Lactobacillales", "Streptococcaceae", "Streptococcus"]}}, {"id": "2", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Gordoniaceae", "Corynebacteriaceae"]}}, {"id": "3", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Staphylococcaceae"]}}, {"id": "4", "metadata": {"taxonomy": ["Bacteria", "Cyanobacteria", "Chloroplasts", "vectors"]}}], "format": "Biological Observation Matrix v0.9", "data": [[0, 0, 42.0], [0, 1, 44536.0], [0, 2, 19111.0], [1, 0, 6.0], [1, 1, 3500.0], [1, 2, 1216.0], [2, 0, 2.0], [2, 1, 1184.0], [2, 2, 1803.0], [3, 0, 17.0], [3, 1, 4903.0], [3, 2, 1722.0], [4, 0, 34.0], [4, 1, 2074.0], [4, 2, 589.0]], "columns": [{"id": "NA", "metadata": null}, {"id": "Key", "metadata": null}, {"id": "Fing", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2572", "matrix_type": "sparse", "shape": [5, 3], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2011-12-21T20:19:06.444921", "type": "OTU table", "id": null, "matrix_element_type": "float"}'
nothing_sorted_otu_table1 = '{"rows": [{"id": "0", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Propionibacterineae", "Propionibacterium"]}}, {"id": "1", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Lactobacillales", "Lactobacillales", "Streptococcaceae", "Streptococcus"]}}, {"id": "2", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Gordoniaceae", "Corynebacteriaceae"]}}, {"id": "3", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Staphylococcaceae"]}}, {"id": "4", "metadata": {"taxonomy": ["Bacteria", "Cyanobacteria", "Chloroplasts", "vectors"]}}], "format": "Biological Observation Matrix v0.9", "data": [[0, 0, 19111.0], [0, 1, 42.0], [0, 2, 44536.0], [1, 0, 1216.0], [1, 1, 6.0], [1, 2, 3500.0], [2, 0, 1803.0], [2, 1, 2.0], [2, 2, 1184.0], [3, 0, 1722.0], [3, 1, 17.0], [3, 2, 4903.0], [4, 0, 589.0], [4, 1, 34.0], [4, 2, 2074.0]], "columns": [{"id": "Fing", "metadata": null}, {"id": "NA", "metadata": null}, {"id": "Key", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2572", "matrix_type": "sparse", "shape": [5, 3], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2011-12-21T20:19:10.397288", "type": "OTU table", "id": null, "matrix_element_type": "float"}'
name_sorted_otu_table1 = '{"rows": [{"id": "0", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Propionibacterineae", "Propionibacterium"]}}, {"id": "1", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Lactobacillales", "Lactobacillales", "Streptococcaceae", "Streptococcus"]}}, {"id": "2", "metadata": {"taxonomy": ["Bacteria", "Actinobacteria", "Actinobacteridae", "Gordoniaceae", "Corynebacteriaceae"]}}, {"id": "3", "metadata": {"taxonomy": ["Bacteria", "Firmicutes", "Alicyclobacillaceae", "Bacilli", "Staphylococcaceae"]}}, {"id": "4", "metadata": {"taxonomy": ["Bacteria", "Cyanobacteria", "Chloroplasts", "vectors"]}}], "format": "Biological Observation Matrix v0.9", "data": [[0, 0, 19111.0], [0, 1, 44536.0], [0, 2, 42.0], [1, 0, 1216.0], [1, 1, 3500.0], [1, 2, 6.0], [2, 0, 1803.0], [2, 1, 1184.0], [2, 2, 2.0], [3, 0, 1722.0], [3, 1, 4903.0], [3, 2, 17.0], [4, 0, 589.0], [4, 1, 2074.0], [4, 2, 34.0]], "columns": [{"id": "Fing", "metadata": null}, {"id": "Key", "metadata": null}, {"id": "NA", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2572", "matrix_type": "sparse", "shape": [5, 3], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2011-12-21T20:19:15.978029", "type": "OTU table", "id": null, "matrix_element_type": "float"}'
# values in 'Age' column sort differently incorrectly if sorted as strings
mapping_f2 = """
#SampleID Name Age Nothing
Fing Blah 11 4
Key Blah 2 5
NA Blah 1 4
IgnoredSample Blah 1 4"""
if __name__ == "__main__":
main()