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
|
// -----------------------------------------------------------------------------------------------------
// 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 <seqan3/std/ranges>
#include <string>
#include <vector>
#include <seqan3/alphabet/nucleotide/all.hpp>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/range/concept.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_join.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include "../iterator_test_template.hpp"
using seqan3::operator""_aa27;
using seqan3::operator""_dna4;
using iterator_type =
decltype(seqan3::views::translate_join(std::declval<std::vector<seqan3::dna4_vector > &>()).begin());
template <>
struct iterator_fixture<iterator_type> : public ::testing::Test
{
using iterator_tag = std::random_access_iterator_tag;
static constexpr bool const_iterable = true;
std::vector<seqan3::dna4_vector > vec{"ACGTACGTACGTA"_dna4, "TCGAGAGCTTTAGC"_dna4};
std::vector<std::vector<seqan3::aa27> > expected_range{{"TYVR"_aa27}, {"RTYV"_aa27}, {"VRT"_aa27}, {"YVRT"_aa27},
{"TYVR"_aa27}, {"RTY"_aa27}, {"SRAL"_aa27}, {"REL*"_aa27},
{"ESFS"_aa27}, {"AKAL"_aa27}, {"LKLS"_aa27}, {"*SSR"_aa27}};
decltype(seqan3::views::translate_join(vec)) test_range = seqan3::views::translate_join(vec);
template <typename A, typename B>
static void expect_eq(A && test_range_value, B && expected_range_value)
{
EXPECT_RANGE_EQ(test_range_value, expected_range_value);
}
};
using test_type = ::testing::Types<iterator_type>;
INSTANTIATE_TYPED_TEST_SUITE_P(iterator_fixture, iterator_fixture, test_type, );
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)
{
std::string const in1{"ACGTACGTACGTA"};
std::string const in2{"TCGAGAGCTTTAGC"};
std::vector<std::vector<TypeParam> > vec;
vec.resize(2);
vec[0] = in1 | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
vec[1] = in2 | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
std::vector<std::vector<seqan3::aa27> > cmp1{{"TYVR"_aa27}, {"SRAL"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp2{{"TYVR"_aa27}, {"YVRT"_aa27}, {"SRAL"_aa27}, {"AKAL"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp3{{"TYVR"_aa27}, {"RTYV"_aa27}, {"VRT"_aa27}, {"SRAL"_aa27},
{"REL*"_aa27}, {"ESFS"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp4{{"TYVR"_aa27}, {"RTYV"_aa27}, {"VRT"_aa27}, {"YVRT"_aa27},
{"TYVR"_aa27}, {"RTY"_aa27}, {"SRAL"_aa27}, {"REL*"_aa27},
{"ESFS"_aa27}, {"AKAL"_aa27}, {"LKLS"_aa27}, {"*SSR"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp5{{"TYVR"_aa27}, {"VRT"_aa27}, {"SRAL"_aa27}, {"ESFS"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp6{{"CMHA"_aa27}, {"MHAC"_aa27}, {"SSRN"_aa27}, {"RFRE"_aa27}};
std::vector<std::vector<seqan3::aa27> > cmp7{{"CMHA"_aa27}};
// default parameter translation_frames
auto v1 = vec | seqan3::views::translate_join;
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y],[S,R,A,L],[R,E,L,*],[E,S,F,S],[A,K,A,L],[L,K,L,S],[*,S,S,R]]
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_join();
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y],[S,R,A,L],[R,E,L,*],[E,S,F,S],[A,K,A,L],[L,K,L,S],[*,S,S,R]]
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_join(seqan3::translation_frames::FWD_FRAME_0);
// == [[T,Y,V,R],[S,R,A,L]]
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_join(seqan3::translation_frames::FWD_REV_0);
// == [[T,Y,V,R],Y,V,R,T],[S,R,A,L],[A,K,A,L]]
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_join(seqan3::translation_frames::FWD);
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[S,R,A,L],[R,E,L,*],[E,S,F,S]]
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_join(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],[S,R,A,L],[R,E,L,*],[E,S,F,S],[A,K,A,L],[L,K,L,S],[*,S,S,R]]
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_join(seqan3::translation_frames::FWD_FRAME_0
| seqan3::translation_frames::FWD_FRAME_2);
// == [[T,Y,V,R],[V,R,T],[S,R,A,L],[E,S,F,S]]
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_join(vec, seqan3::translation_frames::FWD_REV_0);
// == [[T,Y,V,R],[R,T,Y,V],[V,R,T],[Y,V,R,T],[T,Y,V,R],[R,T,Y],[S,R,A,L], [R,E,L,*], [E,S,F,S], [A,K,A,L], [L,K,L,S], [*,S,S,R]]
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_join(seqan3::translation_frames::FWD_REV_0);
// == [[C,M,H,A],[M,H,A,C],[S,S,R,N],[R,F,R,E]]
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_join(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_join(seqan3::views::complement(vec),
seqan3::translation_frames::FWD_REV_0);
// == [[C,M,H,A],[M,H,A,C],[S,S,R,N],[R,F,R,E]]
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_concepts)
{
std::string const in1{"ACGTACGTACGTA"};
std::string const in2{"TCGAGAGCTTTAGC"};
std::vector<std::vector<TypeParam> > vec;
vec.resize(2);
vec[0] = in1 | seqan3::views::char_to<TypeParam> | seqan3::views::to<std::vector>;
vec[1] = in2 | 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_join(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)>>);
}
|
