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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
|
// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#include <gtest/gtest.h>
#include <iostream>
#include <string>
#include <vector>
#include <seqan3/alphabet/nucleotide/all.hpp>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/range/concept.hpp>
#include <seqan3/range/container/concatenated_sequences.hpp>
#include <seqan3/range/views/char_to.hpp>
#include <seqan3/range/views/complement.hpp>
#include <seqan3/range/views/to.hpp>
#include <seqan3/range/views/translate.hpp>
#include <seqan3/std/algorithm>
#include <seqan3/std/ranges>
#include <seqan3/test/expect_range_eq.hpp>
using seqan3::operator""_aa27;
template <typename T>
class nucleotide : public ::testing::Test
{};
// add all alphabets here
using nucleotide_types = ::testing::Types<seqan3::dna4,
seqan3::dna5,
seqan3::dna15,
seqan3::rna4,
seqan3::rna5,
seqan3::rna15>;
TYPED_TEST_SUITE(nucleotide, nucleotide_types, );
TYPED_TEST(nucleotide, view_translate_single)
{
std::string const in{"ACGTACGTACGTA"};
std::vector<TypeParam> vec = in | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
seqan3::aa27_vector cmp1{"TYVR"_aa27};
seqan3::aa27_vector cmp2{"CMHA"_aa27};
seqan3::aa27_vector cmp3{"AHMC"_aa27};
// default parameter translation_frames
auto v1 = vec | seqan3::views::translate_single;
// == [T,Y,V,R]
EXPECT_RANGE_EQ(v1, cmp1);
// default parameter translation_frames
auto v2 = vec | seqan3::views::translate_single();
// == [T,Y,V,R]
EXPECT_RANGE_EQ(v2, cmp1);
// single frame translation
auto v3 = vec | seqan3::views::translate_single(seqan3::translation_frames::FWD_FRAME_0);
// == [T,Y,V,R]
EXPECT_RANGE_EQ(v3, cmp1);
// function syntax
auto v4 = seqan3::views::translate_single(vec, seqan3::translation_frames::FWD_FRAME_0);
// == [T,Y,V,R]
EXPECT_RANGE_EQ(v4, cmp1);
// combinability
auto v5 = vec
| seqan3::views::complement
| seqan3::views::translate_single(seqan3::translation_frames::FWD_FRAME_0);
// == [C,M,H,A]
EXPECT_RANGE_EQ(v5, cmp2);
// combinability
auto v6 = vec
| seqan3::views::complement
| seqan3::views::translate_single(seqan3::translation_frames::FWD_FRAME_0)
| std::views::reverse;
// == [A,H,M,C]
EXPECT_RANGE_EQ(v6, cmp3);
}
TYPED_TEST(nucleotide, view_translate)
{
std::string const in{"ACGTACGTACGTA"};
std::vector<TypeParam> vec = in | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
std::vector<std::vector<seqan3::aa27> > cmp1{{"TYVR"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp2{{"TYVR"_aa27}, {"YVRT"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp3{{"TYVR"_aa27}, {"RTYV"_aa27}, {"VRT"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp4{{"TYVR"_aa27}, {"RTYV"_aa27}, {"VRT"_aa27}, {"YVRT"_aa27},
{"TYVR"_aa27}, {"RTY"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp5{{"TYVR"_aa27}, {"VRT"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp6{{"CMHA"_aa27}, {"MHAC"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp7{{"CMHA"_aa27}};
// default parameter translation_frames
auto v1 = vec | seqan3::views::translate;
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y]]
EXPECT_EQ(v1.size(), cmp4.size());
for (unsigned i = 0; i < v1.size(); i++)
EXPECT_RANGE_EQ(v1[i], cmp4[i]);
// default parameter translation_frames
auto v2 = vec | seqan3::views::translate();
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y]]
EXPECT_EQ(v2.size(), cmp4.size());
for (unsigned i = 0; i < v2.size(); i++)
EXPECT_RANGE_EQ(v2[i], cmp4[i]);
// single frame translation
auto v3 = vec | seqan3::views::translate(seqan3::translation_frames::FWD_FRAME_0);
// == [[T,Y,V,R]]
EXPECT_EQ(v3.size(), cmp1.size());
for (unsigned i = 0; i < v3.size(); i++)
EXPECT_RANGE_EQ(v3[i], cmp1[i]);
// reverse translation
auto v4 = vec | seqan3::views::translate(seqan3::translation_frames::FWD_REV_0);
// == [[T,Y,V,R],[Y,V,R,T]]
EXPECT_EQ(v4.size(), cmp2.size());
for (unsigned i = 0; i < v4.size(); i++)
EXPECT_RANGE_EQ(v4[i], cmp2[i]);
// forward frames translation
auto v5 = vec | seqan3::views::translate(seqan3::translation_frames::FWD);
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T]]
EXPECT_EQ(v5.size(), cmp3.size());
for (unsigned i = 0; i < v5.size(); i++)
EXPECT_RANGE_EQ(v5[i], cmp3[i]);
// six frame translation
auto v6 = vec | seqan3::views::translate(seqan3::translation_frames::SIX_FRAME);
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y]]
EXPECT_EQ(v6.size(), cmp4.size());
for (unsigned i = 0; i < v6.size(); i++)
EXPECT_RANGE_EQ(v6[i], cmp4[i]);
// user-defined frame combination
auto v7 = vec | seqan3::views::translate(seqan3::translation_frames::FWD_FRAME_0
| seqan3::translation_frames::FWD_FRAME_2);
// == [[T,Y,V,R],[V,R,T]]
EXPECT_EQ(v7.size(), cmp5.size());
for (unsigned i = 0; i < v7.size(); i++)
EXPECT_RANGE_EQ(v7[i], cmp5[i]);
// function syntax
auto v8 = seqan3::views::translate(vec, seqan3::translation_frames::FWD_REV_0);
// == [[T,Y,V,R],[Y,V,R,T]]
EXPECT_EQ(v8.size(), cmp2.size());
for (unsigned i = 0; i < v8.size(); i++)
EXPECT_RANGE_EQ(v8[i], cmp2[i]);
// combinability
auto v9 = vec | seqan3::views::complement | seqan3::views::translate(seqan3::translation_frames::FWD_REV_0);
// == [[C,M,H,A],[M,H,A,C]]
EXPECT_EQ(v9.size(), cmp6.size());
for (unsigned i = 0; i < v9.size(); i++)
EXPECT_RANGE_EQ(v9[i], cmp6[i]);
// combinability
auto v10 = vec
| seqan3::views::complement
| seqan3::views::translate(seqan3::translation_frames::FWD_REV_0)
| std::views::take(1);
// == [[C,M,H,A]]
EXPECT_EQ(v10.size(), cmp7.size());
for (unsigned i = 0; i < v10.size(); i++)
EXPECT_RANGE_EQ(v10[i], cmp7[i]);
// combinability and function syntax
auto v11 = seqan3::detail::view_translate(seqan3::views::complement(vec), seqan3::translation_frames::FWD_REV_0);
// == [[C,M,H,A],[M,H,A,C]]
EXPECT_EQ(v11.size(), cmp6.size());
for (unsigned i = 0; i < v11.size(); i++)
EXPECT_RANGE_EQ(v11[i], cmp6[i]);
}
TYPED_TEST(nucleotide, view_translate_single_container_conversion)
{
std::string const in{"ACGTACGTACGTA"};
std::vector<TypeParam> vec = in | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
seqan3::aa27_vector cmp1{"TYVR"_aa27};
// default parameter translation_frames
auto v1 = vec | seqan3::views::translate_single | seqan3::views::to<std::vector>;
// == [T,Y,V,R]
EXPECT_EQ(std::vector<seqan3::aa27>(v1) , cmp1);
}
TYPED_TEST(nucleotide, view_translate_container_conversion)
{
std::string const in{"ACGTACGTACGTA"};
std::vector<TypeParam> vec = in | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
std::vector<std::vector<seqan3::aa27> > cmp1{{"TYVR"_aa27}, {"RTYV"_aa27}, {"VRT"_aa27}, {"YVRT"_aa27},
{"TYVR"_aa27}, {"RTY"_aa27}};
// six frame translation
auto v1 = vec | seqan3::views::translate(seqan3::translation_frames::SIX_FRAME);
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y]]
EXPECT_EQ(v1.size(), cmp1.size());
for (unsigned i = 0; i < v1.size(); i++)
EXPECT_EQ(v1[i] | seqan3::views::to<std::vector>, cmp1[i]);
EXPECT_TRUE(seqan3::concatenated_sequences<std::vector<seqan3::aa27> >(v1) == cmp1);
}
TYPED_TEST(nucleotide, view_translate_single_concepts)
{
std::string const in{"ACGTACGTACGTA"};
std::vector<TypeParam> vec = in | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
EXPECT_TRUE(std::ranges::input_range<decltype(vec)>);
EXPECT_TRUE(std::ranges::forward_range<decltype(vec)>);
EXPECT_TRUE(std::ranges::random_access_range<decltype(vec)>);
EXPECT_TRUE(std::ranges::sized_range<decltype(vec)>);
auto v1 = vec | seqan3::views::translate_single(seqan3::translation_frames::FWD_FRAME_0);
EXPECT_TRUE(std::ranges::input_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::forward_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::random_access_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::sized_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::view<decltype(v1)>);
EXPECT_TRUE((std::is_same_v<seqan3::aa27, std::ranges::range_value_t<decltype(v1)>>));
EXPECT_TRUE((std::is_same_v<seqan3::aa27, std::ranges::range_reference_t<decltype(v1)>>));
}
TYPED_TEST(nucleotide, view_translate_concepts)
{
std::string const in{"ACGTACGTACGTA"};
std::vector<TypeParam> vec = in | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
EXPECT_TRUE(std::ranges::forward_range<decltype(vec)>);
EXPECT_TRUE(std::ranges::random_access_range<decltype(vec)>);
EXPECT_TRUE(std::ranges::sized_range<decltype(vec)>);
auto v1 = vec | seqan3::views::translate(seqan3::translation_frames::FWD_REV_0);
EXPECT_TRUE(std::ranges::input_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::forward_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::random_access_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::sized_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::view<decltype(v1)>);
EXPECT_TRUE(std::ranges::random_access_range<std::ranges::range_value_t<decltype(v1)>>);
EXPECT_TRUE(std::ranges::sized_range<std::ranges::range_value_t<decltype(v1)>>);
EXPECT_TRUE(std::ranges::view<std::ranges::range_value_t<decltype(v1)>>);
EXPECT_TRUE(std::ranges::random_access_range<std::ranges::range_reference_t<decltype(v1)>>);
EXPECT_TRUE(std::ranges::sized_range<std::ranges::range_reference_t<decltype(v1)>>);
EXPECT_TRUE(std::ranges::view<std::ranges::range_reference_t<decltype(v1)>>);
}
TYPED_TEST(nucleotide, issue1339)
{
// empty input
std::string in{};
std::vector<TypeParam> vec = in | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
auto v = vec | seqan3::views::translate;
auto out_vecvec = v | seqan3::views::to<std::vector<std::vector<seqan3::aa27>>>;
EXPECT_EQ(out_vecvec.size(), 6u);
for (auto & out_vec : out_vecvec)
EXPECT_TRUE(out_vec.empty());
// input of size 1
in = "A";
vec = in | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
v = vec | seqan3::views::translate;
out_vecvec = v | seqan3::views::to<std::vector<std::vector<seqan3::aa27>>>;
EXPECT_EQ(out_vecvec.size(), 6u);
for (auto & out_vec : out_vecvec)
EXPECT_TRUE(out_vec.empty());
}
|
