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Viewing changes to tests/test_pycogent_backports/test_rtax.py

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
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tests/test_pycogent_backports/test_rtax.py
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#!/usr/bin/env python
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3
 
__author__ = "David Soergel"
4
 
__copyright__ = ""
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__credits__ = ["David Soergel"] #remember to add yourself
6
 
__license__ = "GPL"
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__version__ = "1.5.0"
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__maintainer__ = "David Soergel"
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__email__ = "soergel@cs.umass.edu"
10
 
__status__ = "Release"
11
 
 
12
 
from cogent.util.misc import remove_files
13
 
 
14
 
from unittest import TestCase, main
15
 
from qiime.pycogent_backports.rtax import (Rtax, assign_taxonomy)
16
 
from qiime.util import get_tmp_filename
17
 
 
18
 
 
19
 
class RtaxClassifierTests(TestCase):
20
 
    """ Tests of the RTAX classifier module """
21
 
 
22
 
    def setUp(self):
23
 
        self.maxDiff = None
24
 
 
25
 
        self.id_to_taxonomy_fp = get_tmp_filename(\
26
 
         prefix='RtaxTaxonAssignerTests_',suffix='.txt')
27
 
        self.input_seqs_fp = get_tmp_filename(\
28
 
         prefix='RtaxTaxonAssignerTests_',suffix='.fasta')
29
 
        self.reference_seqs_fp = get_tmp_filename(\
30
 
         prefix='RtaxTaxonAssignerTests_',suffix='.fasta')
31
 
        self.read_1_seqs_fp = get_tmp_filename(\
32
 
         prefix='RtaxTaxonAssignerTests_',suffix='.fasta')
33
 
        self.read_2_seqs_fp = get_tmp_filename(\
34
 
         prefix='RtaxTaxonAssignerTests_',suffix='.fasta')
35
 
 
36
 
        self._paths_to_clean_up = [self.id_to_taxonomy_fp,self.input_seqs_fp,self.reference_seqs_fp, self.read_1_seqs_fp,self.read_2_seqs_fp]
37
 
 
38
 
        a = open(self.id_to_taxonomy_fp,'w')
39
 
        a.write(rtax_reference_taxonomy)
40
 
        a.close()
41
 
        b = open(self.reference_seqs_fp,'w')
42
 
        b.write(rtax_reference_fasta)
43
 
        b.close()
44
 
        c = open(self.input_seqs_fp,'w')
45
 
        c.write(rtax_test_repset_fasta)
46
 
        c.close()
47
 
        d = open(self.read_1_seqs_fp,'w')
48
 
        d.write(rtax_test_read1_fasta)
49
 
        d.close()
50
 
        e = open(self.read_2_seqs_fp,'w')
51
 
        e.write(rtax_test_read2_fasta)
52
 
        e.close()
53
 
 
54
 
    def tearDown(self):
55
 
        remove_files(set(self._paths_to_clean_up),error_on_missing=False)
56
 
 
57
 
    def test_paired_end_classification(self):
58
 
        self._paths_to_clean_up += cleanAll(self.read_1_seqs_fp)
59
 
        self._paths_to_clean_up += cleanAll(self.read_2_seqs_fp)
60
 
        result = assign_taxonomy(self.input_seqs_fp, self.reference_seqs_fp, self.id_to_taxonomy_fp, self.read_1_seqs_fp, self.read_2_seqs_fp,single_ok=False,header_id_regex="\\S+\\s+(\\S+?)\/")
61
 
        self.assertEqual(result, rtax_expected_result_paired)
62
 
 
63
 
    def test_paired_end_classification_with_fallback(self):
64
 
        self._paths_to_clean_up += cleanAll(self.read_1_seqs_fp)
65
 
        self._paths_to_clean_up += cleanAll(self.read_2_seqs_fp)
66
 
        result = assign_taxonomy(self.input_seqs_fp, self.reference_seqs_fp, self.id_to_taxonomy_fp, self.read_1_seqs_fp, self.read_2_seqs_fp,single_ok=True,header_id_regex="\\S+\\s+(\\S+?)\/")
67
 
        self.assertEqual(result, rtax_expected_result_paired_with_fallback)
68
 
 
69
 
    def test_single_end_classification(self):
70
 
        self._paths_to_clean_up += cleanAll(self.read_1_seqs_fp)
71
 
        result = assign_taxonomy(self.input_seqs_fp, self.reference_seqs_fp, self.id_to_taxonomy_fp, self.read_1_seqs_fp, None ,header_id_regex="\\S+\\s+(\\S+?)\/")
72
 
        self.assertEqual(result, rtax_expected_result_single)
73
 
 
74
 
 
75
 
def cleanAll(path):
76
 
    return [path, path + ".pos.db",  path + ".pos.dir", path + ".pos.pag", path + ".lines.db", path + ".lines.dir", path + ".lines.pag"]
77
 
 
78
 
 
79
 
# sample data copied from GreenGenes
80
 
 
81
 
 
82
 
rtax_reference_taxonomy = """508720     99.0    k__Bacteria      p__Actinobacteria       c__Actinobacteria       o__Actinomycetales      f__Propionibacteriaceae         g__Propionibacterium    s__Propionibacterium acnes
83
 
508050  99.0    k__Bacteria      p__Proteobacteria       c__Betaproteobacteria   o__Burkholderiales      f__Comamonadaceae       g__Diaphorobacter       s__
84
 
502492  99.0    k__Bacteria      p__Proteobacteria       c__Betaproteobacteria   o__Burkholderiales      f__     g__Aquabacterium        s__
85
 
"""
86
 
 
87
 
rtax_reference_fasta = """>508720
88
 
GACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGCCCTGCTTTTGTGGGGTGCTCGAGTGGCGAACG
89
 
GGTGAGTAACACGTGAGTAACCTGCCCTTGACTTTGGGATAACTTCAGGAAACTGGGGCTAATACCGGATAGGAGCTCCT
90
 
GCTGCATGGTGGGGGTTGGAAAGTTTCGGCGGTTGGGGATGGACTCGCGGCTTATCAGCTTGTTGGTGGGGTAGTGGCTT
91
 
ACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGA
92
 
GGCAGCAGTGGGGAATATTGCACAATGGGCGGAAGCCTGATGCAGCAACGCCGCGTGCGGGATGACGGCCTTCGGGTTGT
93
 
AAACCGCTTTCGCCTGTGACGAAGCGTGAGTGACGGTAATGGGTAAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCG
94
 
GTGATACGTAGGGTGCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGCTCGTAGGTGGTTGATCGCGTCGGAAGTGTAA
95
 
TCTTGGGGCTTAACCCTGAGCGTGCTTTCGATACGGGTTGACTTGAGGAAGGTAGGGGAGAATGGAATTCCTGGTGGAGC
96
 
GGTGGAATGCGCAGATATCAGGAGGAACACCAGTGGCGAAGGCGGTTCTCTGGGCCTTTCCTGACGCTGAGGAGCGAAAG
97
 
CGTGGGGAGCGAACAGGCTTAGATACCCTGGTAGTCCACGCTGTAAACGGTGGGTACTAGGTGTGGGGTCCATTCCACGG
98
 
GTTCCGTGCCGTAGCTAACGCTTTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGG
99
 
GCCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGTAGAACCTTACCTGGGTTTGACATGGATCGGGAG
100
 
TGCTCAGAGATGGGTGTGCCTCTTTTGGGGTCGGTTCACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTT
101
 
GGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTCACTGTTGCCAGCACGTTATGGTGGGGACTCAGTGGAGACCGCCGGG
102
 
GTCAACTCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACGCATGCTACAATGGCTG
103
 
GTACAGAGAGTGGCGAGCCTGTGAGGGTGAGCGAATCTCGGAAAGCCGGTCTCAGTTCGGATTGGGGTCTGCAACTCGAC
104
 
CTCATGAAGTCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGGCT
105
 
>508050
106
 
ATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGTAACAGGTCTTCGGATGCTGACGAGTGGCGAACGGGTG
107
 
AGTAATACATCGGAACGTGCCCGATCGTGGGGGATAACGAGGCGAAAGCTTTGCTAATACCGCATACGATCTACGGATGA
108
 
AAGCGGGGGATCTTCGGACCTCGCGCGGACGGAGCGGCCGATGGCAGATTAGGTAGTTGGTGGGATAAAAGCTTACCAAG
109
 
CCGACGATCTGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC
110
 
AGTGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGCAGGATGAAGGCCTTCGGGTTGTAAACTG
111
 
CTTTTGTACGGAACGAAAAGCCTCTTTCTAATAAAGAGGGGTCATGACGGTACCGTAAGAATAAGCACCGGCTAACTACG
112
 
TGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGTA
113
 
AGACAGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTTTGTGACTGCAAGGCTGGAGTGCGGCAGAGGGGGATGGA
114
 
ATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCGATGGCGAAGGCAATCCCCTGGGCCTGCACTGACG
115
 
CTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTG
116
 
GGTCTTCACTGACTCAGTAACGAAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAG
117
 
GAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCCACCTTTGACA
118
 
TGGCAGGAAGTTTCCAGAGATGGATTCGTGCCCGAAAGGGAACCTGCACACAGGTGCTGCATGGCTGTCGTCAGCTCGTG
119
 
TCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCCATTAGTTGCTACGAAAGGGCACTCTAATGGGACTG
120
 
CCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATAGGTGGGGCTACACACGTCATACAAT
121
 
GGCTGGTACAGAGGGTTGCCAACCCGCGAGGGGGAGCTAATCCCATAAAGCCAGTCGTAGTCCGGATCGCAGTCTGCAAC
122
 
TCGACTGCGTGAAGTCGGAATCGCTAGTAATCGCGGATCAGAATGTCGCGGTGAATACGTTCCCGGGTCT
123
 
>502492
124
 
ATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGTAACGGGTCCTTCGGGATGCCGACGAGTGGCGAACGGG
125
 
TGAGTAATATATCGGAACGTGCCCAGTAGTGGGGGATAACTGCTCGAAAGAGCAGCTAATACCGCATACGACCTGAGGGT
126
 
GAAAGGGGGGGATCGCAAGACCTCTCGCTATTGGAGCGGCCGATATCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCA
127
 
AGGCAACGATCTGTAGTTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCA
128
 
GCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCAATGCCGCGTGCAGGAAGAAGGCCTTCGGGTTGTAAAC
129
 
TGCTTTTGTCAGGGAAGAAATCTTCTGGGCTAATACCCCGGGAGGATGACGGTACCTGAAGAATAAGCACCGGCTAACTA
130
 
CGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGCTTTG
131
 
CAAGACAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGTGACTGCAAGGCTAGAGTACGGCAGAGGGGGATG
132
 
GAATTCCGCGTGTAGCAGTGAAATGCGTAGATATGCGGAGGAACACCAATGGCGAAGGCAATCCCCTGGGCCTGTACTGA
133
 
CGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTGGTTGT
134
 
TGGACGGCTTGCTGTTCAGTAACGAAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAA
135
 
AGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGTTTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGA
136
 
CATGTCAAGAATTCTGCAGAGATGTGGAAGTGCTCGAAAGAGAACTTGAACACAGGTGCTGCATGGCCGTCGTCAGCTCG
137
 
TGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCTACGCAAGAGCACTCTAATGAGAC
138
 
TGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAGGTCCTCATGGCCCTTATGGGTAGGGCTACACACGTCATACA
139
 
ATGGCCGGTACAGAGGGCTGCCAACCCGCGAGGGGGAGCCAATCCCAGAAAACCGGTCGTAGTCCGGATCGTAGTCTGCA
140
 
ACTCGACTGCGTGAAGTCGGAATCGCTAGTAATCGCGGATCAGCTTGCCGCGGTGAATACGTTCCCGGGTCT
141
 
"""
142
 
 
143
 
 
144
 
rtax_test_repset_fasta = """>clusterIdA splitRead1IdA
145
 
ACCAAGGCTTTGACGGGTAGCCGGCCTGAGTGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGA
146
 
>clusterIdB splitRead1IdB
147
 
CCGACGATCTGTAGCTGGTCTGAGAGGATGTTCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC
148
 
>clusterIdC splitRead1IdC
149
 
AGGCAACGATCTGTAGTTGGTCTGAGAGGAGGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCA
150
 
>clusterIdD splitRead1IdD
151
 
AGGCAACGATCTGTAGTTGGTCTGAGAGGAGGACCAGCCACACTGGGACGGGGGGGGGGCCCAGACTCCTACGGGAGGCA
152
 
"""
153
 
 
154
 
# these reads are the 4th and 14th lines from the reference seqs
155
 
 
156
 
#rtax_test_read1_fasta = """>splitRead1IdA ampliconId_34563456/1
157
 
#ACCAAGGCTTTGACGGGTAGCCGGCCTGAGAGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGA
158
 
#>splitRead1IdB ampliconId_
159
 
#CCGACGATCTGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC
160
 
#>splitRead1IdC ampliconId_
161
 
#AGGCAACGATCTGTAGTTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCA
162
 
#"""
163
 
#
164
 
#rtax_test_read2_fasta = """>splitRead2IdA ampliconId_34563456/3
165
 
#GGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTCACTGTTGCCAGCACGTTATGGTGGGGACTCAGTGGAGACCGCCGGG
166
 
#>splitRead2IdB ampliconId_
167
 
#TCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGCCATTAGTTGCTACGAAAGGGCACTCTAATGGGACTG
168
 
#>splitRead2IdC ampliconId_
169
 
#TGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCATTAGTTGCTACGCAAGAGCACTCTAATGAGAC
170
 
#"""
171
 
 
172
 
 
173
 
# these reads are the 4th and 14th lines from the reference seqs, with one nucleotide changed each
174
 
# except D and E, which are unique to one read or the other
175
 
# and F and G, which are just decoys
176
 
 
177
 
rtax_test_read1_fasta = """>splitRead1IdA ampliconId_34563456/1
178
 
ACCAAGGCTTTGACGGGTAGCCGGCCTGAGTGGGTGACCGGCCACATTGGGACTGAGATACGGCCCAGACTCCTACGGGA
179
 
>splitRead1IdB ampliconId_12341234/1
180
 
CCGACGATCTGTAGCTGGTCTGAGAGGATGTTCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGC
181
 
>splitRead1IdC ampliconId_23452345/1
182
 
AGGCAACGATCTGTAGTTGGTCTGAGAGGAGGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCA
183
 
>splitRead1IdD ampliconId_45674567/1
184
 
AGGCAACGATCTGTAGTTGGTCTGAGAGGAGGACCAAAAAAAAAAAGACTGAGACACGGCCCAGACTCCTACGGGAGGCA
185
 
>splitRead1IdF ampliconId_56785678/1
186
 
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
187
 
"""
188
 
 
189
 
rtax_test_read2_fasta = """>splitRead2IdA ampliconId_34563456/3
190
 
GGGTTAAGTCCCGCAACGAGCGCAACCCTTATTCACTGTTGCCAGCACGTTATGGTGGGGACTCAGTGGAGACCGCCGGG
191
 
>splitRead2IdB ampliconId_12341234/3
192
 
TCGTGAGATGTTGGGTTAAGTCCCGCAACGTGCGCAACCCTTGCCATTAGTTGCTACGAAAGGGCACTCTAATGGGACTG
193
 
>splitRead2IdC ampliconId_23452345/3
194
 
TGTCGTGAGATGTTGGGTTAAGTCCCGCAAAGAGCGCAACCCTTGTCATTAGTTGCTACGCAAGAGCACTCTAATGAGAC
195
 
>splitRead2IdE ampliconId_67896789/3
196
 
TGTCGTGAGATGTTGGGTTAAAAAAAAAAAAAAACGCAACCCTTGTCATTAGTTGCTACGCAAGAGCACTCTAATGAGAC
197
 
>splitRead2IdG ampliconId_78907890/3
198
 
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
199
 
"""
200
 
 
201
 
 
202
 
rtax_expected_result_paired = {
203
 
    'clusterIdA splitRead1IdA': ('k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__Propionibacterium acnes', 1.0),
204
 
    'clusterIdB splitRead1IdB': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Diaphorobacter; s__', 1.0),
205
 
    'clusterIdC splitRead1IdC': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0),
206
 
    }
207
 
 
208
 
rtax_expected_result_paired_with_fallback = {
209
 
    'clusterIdA splitRead1IdA': ('k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__Propionibacterium acnes', 1.0),
210
 
    'clusterIdB splitRead1IdB': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Diaphorobacter; s__', 1.0),
211
 
    'clusterIdC splitRead1IdC': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0),
212
 
    'clusterIdD splitRead1IdD': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0),
213
 
    }
214
 
 
215
 
rtax_expected_result_single = {
216
 
    'clusterIdA splitRead1IdA': ('k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__Propionibacterium acnes', 1.0),
217
 
    'clusterIdB splitRead1IdB': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Diaphorobacter; s__', 1.0),
218
 
    'clusterIdC splitRead1IdC': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0),
219
 
    'clusterIdD splitRead1IdD': ('k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__; g__Aquabacterium; s__', 1.0),
220
 
    }
221
 
 
222
 
if __name__ == "__main__":
223
 
    main()
224
 
 
225