-
Notifications
You must be signed in to change notification settings - Fork 29
/
Copy pathtest-is.genome.available.R
182 lines (146 loc) · 7.83 KB
/
test-is.genome.available.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
context("Test: is.genome.available()")
test_that("The is.genome.available() interface to NCBI RefSeq
works properly..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'refseq' works properly
expect_equal(nrow(is.genome.available(db = "refseq",
organism = "Saccharomyces cerevisiae",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "refseq",
organism = "Saccharomyces cerevisiae",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI RefSeq
works properly using taxid..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'refseq' works properly
expect_equal(nrow(is.genome.available(db = "refseq",
organism = "559292",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "refseq",
organism = "559292",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI RefSeq
works properly using assembly accession id", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'refseq' works properly
expect_equal(nrow(is.genome.available(db = "refseq",
organism = "GCF_000146045.2",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "refseq",
organism = "GCF_000146045.2",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI Genbank
works properly..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'genbank' works properly
expect_equal(nrow(is.genome.available(db = "genbank",
organism = "Saccharomyces cerevisiae",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "genbank",
organism = "Saccharomyces cerevisiae",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI Genbank
works properly using taxid..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'genbank' works properly
expect_equal(nrow(is.genome.available(db = "genbank",
organism = "559292",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "genbank",
organism = "559292",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI Genbank
works properly using assembly accession id", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'genbank' works properly
expect_equal(nrow(is.genome.available(db = "genbank",
organism = "GCA_000091065.2",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "genbank",
organism = "GCA_000091065.2",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to Ensembl
works properly..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'ensembl' works properly
expect_equal(nrow(is.genome.available(db = "ensembl",
organism = "Saccharomyces cerevisiae",
details = TRUE)) > 0, TRUE)
# test whether interface to 'ensembl' works properly without details
expect_equal(suppressMessages(is.genome.available(db = "ensembl",
organism = "Saccharomyces cerevisiae")), TRUE)
})
test_that("The is.genome.available() interface to Ensembl
works properly using taxid..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'ensembl' works properly
expect_equal(nrow(is.genome.available(db = "ensembl",
organism = "4932",
details = TRUE)) > 0, TRUE)
# test whether interface to 'ensembl' works properly without details
expect_equal(suppressMessages(is.genome.available(db = "ensembl",
organism = "4932")), TRUE)
})
test_that("The is.genome.available() interface to Ensembl
works properly using accession id", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'ensembl' works properly
expect_equal(nrow(is.genome.available(db = "ensembl",
organism = "GCA_000146045.2",
details = TRUE)) > 0, TRUE)
# test whether interface to 'ensembl' works properly without details
expect_equal(suppressMessages(is.genome.available(db = "ensembl",
organism = "GCA_000146045.2")), TRUE)
})
test_that("The is.genome.available() error messages work properly..", {
skip_on_cran()
skip_on_travis()
# test unknown organism error handling for 'refseq'
expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi",
db = "refseq")),
FALSE)
# test unknown organism error handling for 'genbank'
expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi",
db = "genbank")),
FALSE)
# test unknown organism error handling for 'ensembl'
expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi", db = "ensembl")),
FALSE)
expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi", db = "uniprot")),
FALSE)
})
test_that("The is.genome.available() interface to Uniprot
works properly..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'uniprot' works properly
out1 <- is.genome.available(db = "uniprot",
organism = "Saccharomyces cerevisiae",
details = TRUE)
# test whether interface to 'uniprot' works properly without details
out2 <- is.genome.available(db = "uniprot",
organism = "Saccharomyces cerevisiae")
expect_true(nrow(out1) > 0)
expect_true(out2)
})