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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"]
__license__ = "GPL"
__version__ = "1.4.0"
__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_otu_table, parse_mapping_file
from qiime.sort import (sort_sample_ids_by_mapping_value,
sort_fasta_by_abundance, natsort, sort_otu_table,
sort_otu_table_by_mapping_field)
class SortTests(TestCase):
def setUp(self):
self.mapping_f1 = mapping_f1.split('\n')
self.otu_table1 = otu_table1.split('\n')
self.mapping_f2 = mapping_f2.split('\n')
self.age_sorted_otu_table1 = age_sorted_otu_table1.split('\n')
self.name_sorted_otu_table1 = name_sorted_otu_table1.split('\n')
self.nothing_sorted_otu_table1 = nothing_sorted_otu_table1.split('\n')
self.otu_table1_bad_sampleID = otu_table1_bad_sampleID.split('\n')
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_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_otu_table(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Age")
expected = parse_otu_table(self.age_sorted_otu_table1)
# sample ids match expected
self.assertEqual(actual[0],expected[0])
# otu ids match expected
self.assertEqual(actual[1],expected[1])
# otu data match expected
self.assertEqual(actual[2],expected[2])
# taxa match expected
self.assertEqual(actual[3],expected[3])
def test_sort_otu_table(self):
""" sort_otu_table fns as expected """
actual = sort_otu_table(parse_otu_table(self.otu_table1),
['NA','Key','Fing'])
expected = parse_otu_table(self.age_sorted_otu_table1)
# sample ids match expected
self.assertEqual(actual[0],expected[0])
# otu ids match expected
self.assertEqual(actual[1],expected[1])
# otu data match expected
self.assertEqual(actual[2],expected[2])
# taxa match expected
self.assertEqual(actual[3],expected[3])
def test_sort_otu_table_error(self):
""" sort_otu_table handles errors """
self.assertRaises(ValueError,sort_otu_table,
parse_otu_table(self.otu_table1),['NA','Key','Fing','Key'])
self.assertRaises(KeyError,sort_otu_table,
parse_otu_table(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_otu_table(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Nothing")
expected = parse_otu_table(self.nothing_sorted_otu_table1)
# sample ids match expected
self.assertEqual(actual[0],expected[0])
# otu ids match expected
self.assertEqual(actual[1],expected[1])
# otu data match expected
self.assertEqual(actual[2],expected[2])
# taxa match expected
self.assertEqual(actual[3],expected[3])
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_otu_table(self.otu_table1),
parse_mapping_file(self.mapping_f2),
sort_field = "Name")
expected = parse_otu_table(self.name_sorted_otu_table1)
# sample ids match expected
self.assertEqual(actual[0],expected[0])
# otu ids match expected
self.assertEqual(actual[1],expected[1])
# otu data match expected
self.assertEqual(actual[2],expected[2])
# taxa match expected
self.assertEqual(actual[3],expected[3])
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_otu_table(self.otu_table1_bad_sampleID),
parse_mapping_file(self.mapping_f2),
sort_field = "Age")
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 = """# Some comment
OTU ID Fing Key NA Consensus Lineage
0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
# comment
3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors
"""
otu_table1_bad_sampleID = """# Some comment
OTU ID Fing Key NotInMapping Consensus Lineage
0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
# comment
3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors
"""
age_sorted_otu_table1 = """# Some comment
OTU ID NA Key Fing Consensus Lineage
0 42 44536 19111 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 6 3500 1216 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 2 1184 1803 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
3 17 4903 1722 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 34 2074 589 Bacteria; Cyanobacteria; Chloroplasts; vectors
"""
nothing_sorted_otu_table1 = """# Some comment
OTU ID Fing NA Key Consensus Lineage
0 19111 42 44536 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 1216 6 3500 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 2 1184 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
3 1722 17 4903 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 34 2074 Bacteria; Cyanobacteria; Chloroplasts; vectors
"""
name_sorted_otu_table1 = """# Some comment
OTU ID Fing Key NA Consensus Lineage
0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors
"""
# 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()
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