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#!/usr/bin/env python
"""Tests of code for assigning taxonomy"""
__author__ = "Dan Knights"
__copyright__ = "Copyright 2011, The QIIME Project"
#remember to add yourself if you make changes
__credits__ = ["Dan Knights"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Dan Knights"
__email__ = "daniel.knights@colorado.edu"
__status__ = "Release"
from os import remove, system, mkdir
from shutil import rmtree
from os.path import join, exists
from tempfile import NamedTemporaryFile, mkdtemp
from cogent.util.unit_test import TestCase, main
from cogent.app.util import ApplicationError
from qiime.util import get_tmp_filename
from cogent.util.misc import remove_files
from qiime.supervised_learning import RSupervisedLearner
from numpy import array
def is_float(input_string):
"""True if string can be cast as a float"""
try:
float(input_string)
return True
except ValueError:
return False
class RSupervisedLearnerTests(TestCase):
"""Tests of the RSupervisedLearner class"""
def setUp(self):
# Temporary input file
self.tmp_otu_filepath = get_tmp_filename(
prefix='R_test_otu_table_',
suffix='.txt'
)
seq_file = open(self.tmp_otu_filepath, 'w')
seq_file.write(test_otu_table)
seq_file.close()
self.tmp_map_filepath = get_tmp_filename(
prefix='R_test_map_',
suffix='.txt'
)
seq_file = open(self.tmp_map_filepath, 'w')
seq_file.write(test_map)
seq_file.close()
self.files_to_remove = \
[self.tmp_otu_filepath, self.tmp_map_filepath]
# Prep input files in R format
output_dir = mkdtemp()
self.dirs_to_remove = [output_dir]
# get random forests results
mkdir(join(output_dir, 'random_forest'))
self.results = RSupervisedLearner()(
self.tmp_otu_filepath, self.tmp_map_filepath,'Individual',
ntree=100, errortype='oob',
output_dir=output_dir)
def tearDown(self):
remove_files(set(self.files_to_remove))
# remove directories last, so we don't get errors
# trying to remove files which may be in the directories
for d in self.dirs_to_remove:
if exists(d):
rmtree(d)
def test_features_format(self):
results = self.results
features_output = results['features'].readlines()
# ensure that at least one feature is listed (skip header and comment)
num_features_returned = len(features_output) - 1
self.assertGreaterThan(num_features_returned, 0)
# ensure that each line has two elements, and that the first one
# is the name of one of the OTUs, the second is a float
for line in features_output[1:]:
words = line.strip().split('\t')
line_length = len(words)
self.assertEqual(line_length, 3)
self.assertEqual(words[0] in test_OTU_IDs, True)
self.assertEqual(is_float(words[1]), True)
def test_cv_probabilities_format(self):
results = self.results
# verify FORMAT of cross-validation probabilities file
probabilities_output = results['cv_probabilities'].readlines()
# ensure that all input samples were predicted
num_samples_returned = len(probabilities_output)-1
self.assertEqual(num_samples_returned, len(test_sample_IDs))
# ensure that each line has five elements, and that the first one
# is the name of one of the samples, the others are floats
for line in probabilities_output[1:]:
words = line.strip().split('\t')
line_length = len(words)
self.assertEqual(line_length, 4)
self.assertEqual(words[0] in test_sample_IDs, True)
for word in words[1:3]:
self.assertEqual(is_float(word),True)
def test_mislabeling_format(self):
results = self.results
# verify FORMAT of mislabeling predictions file
mislabeling_output = results['mislabeling'].readlines()
# ensure that all input samples were predicted
num_samples_returned = len(mislabeling_output)-1
self.assertEqual(num_samples_returned, len(test_sample_IDs))
# ensure that each line has five elements, and that the first one
# is the name of one of the samples, the others are floats
exp = "SampleID\tP(alleged label)\tP(second best)\tP(alleged label)-P(second best)"
self.assertEqual(mislabeling_output[0].strip(), exp)
for line in mislabeling_output[1:]:
words = line.strip().split('\t')
line_length = len(words)
self.assertEqual(line_length, 4)
self.assertEqual(words[0] in test_sample_IDs, True)
for word in words[1:3]:
self.assertEqual(is_float(word),True)
def test_summary_file(self):
results = self.results
# verify summary file (except don't explicitly test error value)
summary_output = results['summary'].readlines()
# check generalization error as a float
result_error = summary_output[2].strip().split('\t')
self.assertEqual(is_float(result_error[1]), True)
# make sure error is between 0 and 1
assert(float(result_error[1]) >= 0)
assert(float(result_error[1]) <= 1)
test_sample_IDs = ['S1RingL', 'S1keyM', 'S1keySpace', 'S1IndexL', 'S1keyK', 'S1ThumbR', 'S1keyV', 'S1IndexR', 'S1keyA', 'S1RingR', 'S1MiddleR', 'S1keyD', 'S2keySpace', 'S2keyJ', 'S2keyLeftShift', 'S2keyN', 'S2keyZ', 'S2IndexL', 'S2keyA', 'S2PinkyL', 'S2keyK', 'S2keyRightShift', 'S2keyM', 'S2keyI', 'S2PinkyR', 'S3keySpace', 'S3keyEnter', 'S3keyS', 'S3IndexR', 'S3ThumbR', 'S3MiddleR', 'S3keyY', 'S3ThumbL', 'S3keyF', 'S3IndexL', 'S3keyW', 'S3keyQ', 'S3keyL']
test_OTU_IDs = ['88', '131', '144', '158', '193', '225', '260', '588', '634', '721', '821', '843', '883', '891', '976', '979', '983', '1035', '1088', '1156', '1287', '1314', '1351', '1373', '1487', '1582', '1591', '1784', '1848', '1886', '2007', '2059', '2096', '2187', '2218', '2270', '2328', '2360', '2366', '2407', '2519', '2526', '2810', '2915', '2932', '2956', '3006', '3060', '3108', '3127']
test_otu_table = """#Full OTU Counts
#OTU ID S1RingL S1keyM S1keySpace S1IndexL S1keyK S1ThumbR S1keyV S1IndexR S1keyA S1RingR S1MiddleR S1keyD S2keySpace S2keyJ S2keyLeftShift S2keyN S2keyZ S2IndexL S2keyA S2PinkyL S2keyK S2keyRightShift S2keyM S2keyI S2PinkyR S3keySpace S3keyEnter S3keyS S3IndexR S3ThumbR S3MiddleR S3keyY S3ThumbL S3keyF S3IndexL S3keyW S3keyQ S3keyL Consensus Lineage
88 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 2 0 3 4 3 0 0 1 5 3 3 1 1 1 1 2 1 0 0 0 1 0 1 Aa;other
131 0 0 0 0 0 0 0 0 0 1 0 0 1 1 1 0 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Ab;other
144 0 0 0 0 0 0 0 0 0 0 0 0 2 1 4 0 2 4 6 7 0 0 0 2 4 0 0 0 0 0 0 0 0 0 0 0 0 1 Ac;other
158 0 0 0 0 0 0 0 0 0 0 0 0 2 1 3 5 0 1 7 6 1 1 0 1 3 0 1 1 0 0 0 0 0 0 0 1 0 0 Ad;other
193 2 0 0 0 2 0 0 0 0 0 0 0 3 8 0 1 2 2 1 0 1 3 3 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 Ae;other
225 0 0 0 0 1 0 0 0 3 0 0 2 1 1 0 0 0 0 0 0 0 1 0 1 0 0 2 2 0 3 0 2 0 0 1 0 3 5 Af;other
260 1 0 0 1 0 2 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 Ag;other
588 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 1 0 0 1 0 1 1 0 0 0 0 1 Ah;other
634 0 0 0 0 0 0 0 1 0 0 0 0 3 0 0 2 0 1 1 0 2 2 0 2 0 0 0 0 1 1 0 0 1 0 1 0 1 0 Ai;other
721 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Aj;other
821 5 0 0 1 1 1 1 2 0 3 1 1 6 10 4 5 2 1 6 2 3 3 10 8 3 0 0 1 0 0 0 2 1 1 2 0 1 0 Ak;other
843 1 0 1 3 0 0 0 0 0 0 2 0 2 4 0 2 1 3 4 0 1 2 0 2 3 0 0 0 0 2 0 0 0 0 0 0 0 0 Al;other
883 4 7 3 1 1 3 5 1 1 2 0 5 0 2 3 1 0 1 1 3 14 10 6 3 2 0 0 0 0 0 1 0 0 0 3 0 0 1 Am;other
891 0 1 5 0 0 0 3 0 1 0 0 1 5 3 10 3 5 12 10 8 2 0 3 3 9 0 2 3 8 2 8 2 1 1 1 3 4 2 An;other
976 0 4 0 0 8 0 0 0 0 1 0 1 4 16 2 4 1 0 1 0 1 0 0 3 0 7 2 9 2 3 5 17 6 10 4 7 12 6 Ao;other
979 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 6 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 Ap;other
983 2 1 0 0 0 2 1 0 0 1 1 0 7 0 3 0 0 0 0 0 1 1 0 3 0 0 0 0 0 1 0 0 0 0 0 0 0 0 Aq;other
1035 7 10 4 3 3 19 9 11 10 5 4 13 7 18 7 16 6 21 26 16 8 23 17 9 30 4 7 7 6 6 3 4 2 0 2 10 2 3 Ar;other
1088 0 0 0 0 0 0 0 0 0 0 0 0 2 1 4 1 9 12 7 9 3 2 2 2 9 0 0 0 1 1 2 0 0 0 2 0 0 0 As;other
1156 0 2 2 1 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 At;other
1287 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 1 1 4 2 2 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 Au;other
1314 1 0 0 0 0 1 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Av;other
1351 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 2 3 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Aw;other
1373 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 2 0 1 0 0 1 3 0 Ax;other
1487 0 0 0 0 1 0 1 0 1 0 0 0 9 3 2 3 18 3 3 2 3 5 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 Ay;other
1582 0 0 1 0 0 1 1 1 1 1 1 0 4 3 1 1 1 0 2 0 6 3 3 1 3 0 0 0 1 1 1 0 1 0 1 0 0 1 Az;other
1591 0 0 0 0 0 0 0 0 0 0 0 0 2 3 4 1 0 0 3 1 1 4 1 4 1 0 0 0 1 0 0 0 0 0 0 0 0 0 Ba;other
1784 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 1 0 2 2 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bb;other
1848 150 149 154 58 156 137 153 163 151 157 176 155 16 17 9 38 6 8 3 14 54 37 52 17 29 137 153 140 110 132 97 128 161 177 143 141 126 123 Bc;other
1886 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bd;other
2007 0 0 0 2 0 0 1 0 0 0 0 0 5 8 5 3 1 0 4 0 8 9 5 2 3 0 1 2 0 0 0 0 1 0 0 0 0 1 Be;other
2059 0 0 1 1 0 2 1 0 0 3 1 0 12 2 2 2 1 0 4 0 5 6 2 4 4 14 0 3 23 18 12 11 4 1 4 1 1 4 Bf;other
2096 0 0 0 0 0 1 0 0 2 1 0 0 5 0 8 3 5 43 13 30 1 1 2 3 20 0 0 0 0 0 0 0 0 0 0 0 1 0 Bg;other
2187 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1 2 0 0 0 2 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bh;other
2218 0 0 0 1 0 0 0 0 0 0 0 0 2 1 0 3 0 0 1 1 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bi;other
2270 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 2 1 0 0 0 0 0 0 0 Bj;other
2328 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bk;other
2360 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 0 0 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bl;other
2366 0 1 2 0 0 0 0 0 0 0 0 0 2 8 34 2 2 2 6 35 1 4 4 3 3 1 0 0 0 0 0 1 0 0 0 0 0 0 Bm;other
2407 0 0 0 0 0 0 0 0 0 0 0 0 2 4 1 0 0 7 6 3 2 0 0 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 Bn;other
2519 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 3 2 1 3 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bo;other
2526 0 0 1 0 10 1 0 0 0 2 0 2 5 3 1 2 0 0 2 1 4 2 5 14 7 1 1 2 4 0 14 0 2 2 0 2 2 5 Bp;other
2810 0 0 2 0 0 1 0 0 0 2 0 0 0 0 6 2 0 9 0 3 0 0 0 2 7 3 1 0 2 0 1 0 2 1 3 1 1 0 Bq;other
2915 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 4 1 2 0 0 0 1 3 0 0 0 0 0 0 0 0 0 0 0 1 0 Br;other
2932 2 3 10 96 2 4 7 8 2 5 1 0 18 13 12 39 13 4 16 2 32 21 32 13 8 1 0 2 0 1 5 0 3 0 3 3 3 0 Bs;other
2956 1 0 1 1 0 0 1 1 0 2 1 0 1 1 0 3 0 0 1 0 0 0 2 0 2 1 0 0 0 0 2 0 0 0 0 1 0 0 Bt;other
3006 0 0 0 0 1 0 0 0 0 0 0 0 2 2 3 3 3 19 3 9 0 1 2 5 4 0 1 0 0 0 0 3 0 0 0 0 0 0 Bu;other
3060 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 7 1 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bv;other
3108 0 0 0 0 0 0 0 0 0 0 0 0 3 0 3 0 3 0 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Bw;other
3127 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 2 1 2 0 0 0 0 1 0 0 Bx;other"""
test_map = \
"""#SampleID Digit Hand Keysize Key Source Individual Spacebar SpacebarSex Typingdigit Handkey HandIndiv TypingHand TypingHandSource TypingHandIndiv TypingHandSourceIndiv UseFreq Description
S1RingL Ring Left NA NA Fing S1 NA NA Ri Left S1Left RiLeft RiLeftFing RiLeftS1 RiLeftFingS1 NA S1.ring-left
S1keyM NA NA Small M Key S1 NA NA In Right S1Right InRight InRightKey InRightS1 InRightKeyS1 2to6 S1.key, m
S1keySpace NA NA Large Space Key S1 Private Male Th Mixed S1Mixed ThMixed ThMixedKey ThMixedS1 ThMixedKeyS1 NA S1.key, spacebar
S1IndexL Index Left NA NA Fing S1 NA NA In Left S1Left InLeft InLeftFing InLeftS1 InLeftFingS1 NA S1.index-left
S1keyK NA NA Small K Key S1 NA NA Mi Right S1Right MiRight MiRightKey MiRightS1 MiRightKeyS1 1minus S1.key, k
S1ThumbR Thumb Right NA NA Fing S1 NA NA Th Right S1Right ThRight ThRightFing ThRightS1 ThRightFingS1 NA S1.thumb-right
S1keyV NA NA Small V Key S1 NA NA In Left S1Left InLeft InLeftKey InLeftS1 InLeftKeyS1 1to2 S1.key, v
S1IndexR Index Right NA NA Fing S1 NA NA In Right S1Right InRight InRightFing InRightS1 InRightFingS1 NA S1.index-right
S1keyA NA NA Small A Key S1 NA NA Pi Left S1Left PiLeft PiLeftKey PiLeftS1 PiLeftKeyS1 7plus S1.key, a
S1RingR Ring Right NA NA Fing S1 NA NA Ri Right S1Right RiRight RiRightFing RiRightS1 RiRightFingS1 NA S1.ring-right
S1MiddleR Middle Right NA NA Fing S1 NA NA Mi Right S1Right MiRight MiRightFing MiRightS1 MiRightFingS1 NA S1.middle-right
S1keyD NA NA Small D Key S1 NA NA Mi Left S1Left MiLeft MiLeftKey MiLeftS1 MiLeftKeyS1 2to6 S1.key, d
S2keySpace NA NA Large Space Key S2 Private Male Th Mixed S2Mixed ThMixed ThMixedKey ThMixedS2 ThMixedKeyS2 NA S2.key, spacebar
S2keyJ NA NA Small J Key S2 NA NA In Right S2Right InRight InRightKey InRightS2 InRightKeyS2 1minus S2.key, j
S2keyLeftShift NA NA Medium LeftShift Key S2 NA NA Pi Left S2Left PiLeft PiLeftKey PiLeftS2 PiLeftKeyS2 NA S2.key, shift-left
S2keyN NA NA Small N Key S2 NA NA In Right S2Right InRight InRightKey InRightS2 InRightKeyS2 6to7 S2.key, n
S2keyZ NA NA Small Z Key S2 NA NA Pi Left S2Left PiLeft PiLeftKey PiLeftS2 PiLeftKeyS2 1minus S2.key, z
S2IndexL Index Left NA NA Fing S2 NA NA In Left S2Left InLeft InLeftFing InLeftS2 InLeftFingS2 NA S2.index-left
S2keyA NA NA Small A Key S2 NA NA Pi Left S2Left PiLeft PiLeftKey PiLeftS2 PiLeftKeyS2 7plus S2.key, a
S2PinkyL Pinky Left NA NA Fing S2 NA NA Pi Left S2Left PiLeft PiLeftFing PiLeftS2 PiLeftFingS2 NA S2.pinky-left
S2keyK NA NA Small K Key S2 NA NA Mi Right S2Right MiRight MiRightKey MiRightS2 MiRightKeyS2 1minus S2.key, k
S2keyRightShift NA NA Medium RightShift Key S2 NA NA Pi Right S2Right PiRight PiRightKey PiRightS2 PiRightKeyS2 NA S2.key, shift-right
S2keyM NA NA Small M Key S2 NA NA In Right S2Right InRight InRightKey InRightS2 InRightKeyS2 2to6 S2.key, m
S2keyI NA NA Small I Key S2 NA NA Mi Right S2Right MiRight MiRightKey MiRightS2 MiRightKeyS2 6to7 S2.key, i
S2PinkyR Pinky Right NA NA Fing S2 NA NA Pi Right S2Right PiRight PiRightFing PiRightS2 PiRightFingS2 NA S2.pinky-right
S3keySpace NA NA Large Space Key S3 Private Male Th Mixed S3Mixed ThMixed ThMixedKey ThMixedS3 ThMixedKeyS3 NA S3.key, spacebar
S3keyEnter NA NA Medium Enter Key S3 NA NA Unk Right S3Right UnkRight UnkRightKey UnkRightS3 UnkRightKeyS3 NA S3.key, enter
S3keyS NA NA Small S Key S3 NA NA Ri Left S3Left RiLeft RiLeftKey RiLeftS3 RiLeftKeyS3 6to7 S3.key, s
S3IndexR Index Right NA NA Fing S3 NA NA In Right S3Right InRight InRightFing InRightS3 InRightFingS3 NA S3.index-right
S3ThumbR Thumb Right NA NA Fing S3 NA NA Th Right S3Right ThRight ThRightFing ThRightS3 ThRightFingS3 NA S3.thumb-right
S3MiddleR Middle Right NA NA Fing S3 NA NA Mi Right S3Right MiRight MiRightFing MiRightS3 MiRightFingS3 NA S3.middle-right
S3keyY NA NA Small Y Key S3 NA NA In Right S3Right InRight InRightKey InRightS3 InRightKeyS3 1to2 S3.key, y
S3ThumbL Thumb Left NA NA Fing S3 NA NA Th Left S3Left ThLeft ThLeftFing ThLeftS3 ThLeftFingS3 NA S3.thumb-left
S3keyF NA NA Small F Key S3 NA NA In Left S3Left InLeft InLeftKey InLeftS3 InLeftKeyS3 2to6 S3.key, f
S3IndexL Index Left NA NA Fing S3 NA NA In Left S3Left InLeft InLeftFing InLeftS3 InLeftFingS3 NA S3.index-left
S3keyW NA NA Small W Key S3 NA NA Ri Left S3Left RiLeft RiLeftKey RiLeftS3 RiLeftKeyS3 2to6 S3.key, w
S3keyQ NA NA Small Q Key S3 NA NA Pi Left S3Left PiLeft PiLeftKey PiLeftS3 PiLeftKeyS3 1minus S3.key, q
S3keyL NA NA Small L Key S3 NA NA Ri Right S3Right RiRight RiRightKey RiRightS3 RiRightKeyS3 2to6 S3.key, l"""
#run unit tests if run from command-line
if __name__ == '__main__':
main()
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