Alphabet related views. More...

Collaboration diagram for Views:

Variables
template<alphabet alphabet_type>
auto const	seqan3::views::char_strictly_to
	A view over an alphabet, given a range of characters.

template<alphabet alphabet_type>
auto const	seqan3::views::char_to
	A view over an alphabet, given a range of characters.

auto const	seqan3::views::complement
	A view that converts a range of nucleotides to their complement.

template<typename alphabet_type >
auto const	seqan3::views::rank_to
	A view over an alphabet, given a range of ranks.

auto const	seqan3::views::to_char
	A view that calls seqan3::to_char() on each element in the input range.

auto const	seqan3::views::to_rank
	A view that calls seqan3::to_rank() on each element in the input range.

constexpr auto	seqan3::views::translate
	A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames.

constexpr auto	seqan3::views::translate_join
	A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames. Input and output range are always two-dimensional.

constexpr auto	seqan3::views::trim_quality
	A view that does quality-threshold trimming on a range of seqan3::quality_alphabet.

template<alphabet alphabet_type>
auto const	seqan3::views::validate_char_for
	An identity view that throws if an encountered character is not valid for the given alphabet.

Alphabet related views
constexpr auto	seqan3::views::translate_single
	A view that translates nucleotide into aminoacid alphabet for one of the six frames.

constexpr auto	seqan3::views::minimiser_hash
	Computes minimisers for a range with a given shape, window size and seed.

Detailed Description

Alphabet related views.

See also: Alphabet

Variable Documentation

◆ char_strictly_to

template<alphabet alphabet_type>

auto const seqan3::views::char_strictly_to

inline

A view over an alphabet, given a range of characters.

Template Parameters

urng_t	The type of the range being processed. See below for requirements. [template parameter is omitted in pipe notation]
alphabet_t	The alphabet to convert to; must satisfy seqan3::alphabet.

Parameters

[in] urange The range being processed. [parameter is omitted in pipe notation]

Returns: A range of converted elements. See below for the properties of the returned range.

Exceptions

seqan3::invalid_char_assignment if an invalid character is encountered.

Header File

#include <seqan3/alphabet/views/char_strictly_to.hpp>

This view differs from seqan3::views::chars_to in that it throws an exception if an invalid character conversion happens. See seqan3::char_strictly_to for more details.

View properties

This view is a deep view. Given a range-of-range as input (as opposed to just a range), it will apply the transformation on the innermost range (instead of the outermost range).

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range		preserved
std::ranges::bidirectional_range		preserved
std::ranges::random_access_range		preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range		preserved
std::ranges::common_range		preserved
std::ranges::output_range		lost
std::semiregular		preserved
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::alphabet_char_t<alphabet_t>	`alphabet_t`

See the views submodule documentation for detailed descriptions of the view properties.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/views/char_strictly_to.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    std::string_view str{"ACTTTGATAN"};
    try
    {
        seqan3::debug_stream << (str | seqan3::views::char_strictly_to<seqan3::dna4>); // ACTTTGATA
    }
    catch (seqan3::invalid_char_assignment const &)
    {
        seqan3::debug_stream << "\n[ERROR] Invalid char!\n"; // Will throw on parsing 'N'
    }
}

This entity is experimental and subject to change in the future. Experimental since version 3.2.

◆ char_to

template<alphabet alphabet_type>

auto const seqan3::views::char_to

inline

A view over an alphabet, given a range of characters.

Template Parameters

urng_t	The type of the range being processed. See below for requirements. [template parameter is omitted in pipe notation]
alphabet_t	The alphabet to convert to; must satisfy seqan3::alphabet.

Parameters

[in] urange The range being processed. [parameter is omitted in pipe notation]

Returns: A range of converted elements. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/char_to.hpp>

View properties

This view is a deep view Given a range-of-range as input (as opposed to just a range), it will apply the transformation on the innermost range (instead of the outermost range).

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range		preserved
std::ranges::bidirectional_range		preserved
std::ranges::random_access_range		preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range		preserved
std::ranges::common_range		preserved
std::ranges::output_range		lost
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::alphabet_char_t<alphabet_t>	`alphabet_t`

See the views submodule documentation for detailed descriptions of the view properties.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/views/char_to.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    std::string str{"ACTTTGATAN"};
    seqan3::debug_stream << (str | seqan3::views::char_to<seqan3::dna4>) << '\n'; // ACTTTGATAA
    seqan3::debug_stream << (str | seqan3::views::char_to<seqan3::dna5>) << '\n'; // ACTTTGATAN
}

This entity is stable. Since version 3.1.

◆ complement

auto const seqan3::views::complement

inline

A view that converts a range of nucleotides to their complement.

Template Parameters

urng_t The type of the range being processed. See below for requirements. [template parameter is omitted in pipe notation]

Parameters

[in] urange The range being processed. [parameter is omitted in pipe notation]

Returns: A range of converted elements. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/complement.hpp>

Calls seqan3::nucleotide_alphabet::complement() on every element of the input range.

View properties

This view is a deep view Given a range-of-range as input (as opposed to just a range), it will apply the transformation on the innermost range (instead of the outermost range).

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range		preserved
std::ranges::bidirectional_range		preserved
std::ranges::random_access_range		preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range		preserved
std::ranges::common_range		preserved
std::ranges::output_range		lost
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::nucleotide_alphabet	std::remove_reference_t<std::ranges::range_reference_t<urng_t>>

See the views submodule documentation for detailed descriptions of the view properties.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/views/complement.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna5_vector foo{"ACGTA"_dna5};
 
    // pipe notation
    auto v = foo | seqan3::views::complement;
    seqan3::debug_stream << v << '\n'; // TGCAT
 
    // function notation
    auto v2(seqan3::views::complement(foo));
    seqan3::debug_stream << v2 << '\n'; // TGCAT
 
    // generate the reverse complement:
    auto v3 = foo | seqan3::views::complement | std::views::reverse;
    seqan3::debug_stream << v3 << '\n'; // TACGT
}

This entity is stable. Since version 3.1.

◆ minimiser_hash

constexpr auto seqan3::views::minimiser_hash

inlineconstexpr

Computes minimisers for a range with a given shape, window size and seed.

Template Parameters

urng_t The type of the range being processed. See below for requirements. [template parameter is omitted in pipe notation]

Parameters

[in]	urange	The range being processed. [parameter is omitted in pipe notation]
[in]	shape	The seqan3::shape that determines how to compute the hash value.
[in]	window_size	The window size to use.
[in]	seed	The seed used to skew the hash values. Default: 0x8F3F73B5CF1C9ADE.

Returns: A range of size_t where each value is the minimiser of the resp. window. See below for the properties of the returned range.

A sequence can be presented by a small number of k-mers (minimisers). For a given shape and window size all k-mers are determined in the forward strand and the backward strand and only the lexicographically smallest k-mer is returned for one window. This process is repeated over every possible window of a sequence. If consecutive windows share a minimiser, it is saved only once. For example, in the sequence "TAAAGTGCTAAA" for an ungapped shape of length 3 and a window size of 5 the first, the second and the last window contain the same minimiser "AAA". Because the minimisers of the first two consecutive windows also share the same position, storing this minimiser twice is redundant and it is stored only once. The "AAA" minimiser of the last window on the other hand is stored, since it is located at an other position than the previous "AAA" minimiser and hence storing the second "AAA"-minimiser is not redundant but necessary.

Non-lexicographical Minimisers by skewing the hash value with a seed

It might happen that a minimiser changes only slightly when sliding the window over the sequence. For instance, when a minimiser starts with a repetition of A’s, then in the next window it is highly likely that the minimiser will start with a repetition of A’s as well. Because it is only one A shorter, depending on how long the repetition is this might go on for multiple window shifts. Saving these only slightly different minimiser makes no sense because they contain no new information about the underlying sequence. Additionally, sequences with a repetition of A’s will be seen as more similar to each other than they actually are. As Marçais et al. have shown, randomizing the order of the k-mers can solve this problem. Therefore, a random seed is used to XOR all k-mers, thereby randomizing the order. The user can change the seed to any other value he or she thinks is useful. A seed of 0 is returning the lexicographical order.

See also: seqan3::views::minimiser_view

Attention: Be aware of the requirements of the seqan3::views::kmer_hash view.

This entity is experimental and subject to change in the future.

View properties

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range	required	preserved
std::ranges::bidirectional_range		lost
std::ranges::random_access_range		lost
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range		lost
std::ranges::common_range		lost
std::ranges::output_range		lost
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::semialphabet	std::size_t

See the views submodule documentation for detailed descriptions of the view properties.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/search/views/minimiser_hash.hpp>
 
using namespace seqan3::literals;
 
int main()
{
    std::vector<seqan3::dna4> text{"CCACGTCGACGGTT"_dna4};
 
    // Here a consecutive shape with size 4 (so the k-mer size is 4) and a window size of 8 is used. The seed is set
    // to 0, so lexicographical ordering is used for demonstration purposes.
    auto minimisers =
        text
        | seqan3::views::minimiser_hash(seqan3::shape{seqan3::ungapped{4}}, seqan3::window_size{8}, seqan3::seed{0});
    seqan3::debug_stream << minimisers << '\n';
    // This leads to [27,97,26,22,5] representing the k-mers [ACGT, CGAC, ACGG, accg, aacc], smaller case k-mers are
    // coming from the reverse strand.
 
    // Here a gapped shape with size 5 (and a k-mer size of 3) and a window size of 8 is used. The seed is set
    // to 0, so lexicographical ordering is used for demonstration purposes.
    auto minimisers2 = text | seqan3::views::minimiser_hash(0b10101_shape, seqan3::window_size{8}, seqan3::seed{0});
    seqan3::debug_stream << minimisers2 << '\n';
    // This leads to [9, 18, 7, 6] representing the k-mers [A.G.C, C.A.G, a.c.t, a.c.g]
}

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ rank_to

template<typename alphabet_type >

auto const seqan3::views::rank_to

inline

A view over an alphabet, given a range of ranks.

Template Parameters

urng_t	The type of the range being processed. See below for requirements. [template parameter is omitted in pipe notation]
alphabet_t	The alphabet to convert to; must satisfy seqan3::writable_semialphabet.

Parameters

[in] urange The range being processed. [parameter is omitted in pipe notation]

Returns: A range of converted elements. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/rank_to.hpp>

View properties

This view is a deep view Given a range-of-range as input (as opposed to just a range), it will apply the transformation on the innermost range (instead of the outermost range).

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range		preserved
std::ranges::bidirectional_range		preserved
std::ranges::random_access_range		preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range		preserved
std::ranges::common_range		preserved
std::ranges::output_range		lost
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::alphabet_rank_t<alphabet_t>	`alphabet_t`

See the views submodule documentation for detailed descriptions of the view properties.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/views/rank_to.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    std::vector<int> vec{0, 1, 3, 3, 3, 2, 0, 3, 0};
    seqan3::debug_stream << (vec | seqan3::views::rank_to<seqan3::dna4>) << '\n'; // ACTTTGATA
    seqan3::debug_stream << (vec | seqan3::views::rank_to<seqan3::dna5>) << '\n'; // ACNNNGANA
}

This entity is stable. Since version 3.1.

◆ to_char

auto const seqan3::views::to_char

inline

A view that calls seqan3::to_char() on each element in the input range.

Template Parameters

urng_t The type of the range being processed. See below for requirements. [template parameter is omitted in pipe notation]

Parameters

[in] urange The range being processed. [parameter is omitted in pipe notation]

Returns: A range of converted elements. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/to_char.hpp>

View properties

This view is a deep view Given a range-of-range as input (as opposed to just a range), it will apply the transformation on the innermost range (instead of the outermost range).

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range		preserved
std::ranges::bidirectional_range		preserved
std::ranges::random_access_range		preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range		preserved
std::ranges::common_range		preserved
std::ranges::output_range		lost
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::alphabet	seqan3::alphabet_char_t<std::ranges::range_value_t<urng_t>>

See the views submodule documentation for detailed descriptions of the view properties.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/quality/aliases.hpp> // includes seqan3::dna4q
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/views/to_char.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna4_vector vec = "ACTTTGATA"_dna4;
    auto v = vec | seqan3::views::to_char;
    seqan3::debug_stream << v << '\n'; // [A,C,T,T,T,G,A,T,A]
 
    std::vector<seqan3::phred42> qvec{seqan3::phred42{}.assign_phred(0),
                                      seqan3::phred42{}.assign_phred(7),
                                      seqan3::phred42{}.assign_phred(5),
                                      seqan3::phred42{}.assign_phred(3),
                                      seqan3::phred42{}.assign_phred(7),
                                      seqan3::phred42{}.assign_phred(4),
                                      seqan3::phred42{}.assign_phred(30),
                                      seqan3::phred42{}.assign_phred(16),
                                      seqan3::phred42{}.assign_phred(23)};
    auto v3 = qvec | seqan3::views::to_char;
    seqan3::debug_stream << v3 << '\n'; // [!,(,&,$,(,%,?,1,8]
 
    std::vector<seqan3::dna4q> qcvec{{'C'_dna4, '!'_phred42},
                                     {'A'_dna4, '('_phred42},
                                     {'G'_dna4, '&'_phred42},
                                     {'T'_dna4, '$'_phred42},
                                     {'G'_dna4, '('_phred42},
                                     {'A'_dna4, '%'_phred42},
                                     {'C'_dna4, '?'_phred42},
                                     {'T'_dna4, '1'_phred42},
                                     {'A'_dna4, '8'_phred42}};
    auto v4 = qcvec | seqan3::views::to_char;
    seqan3::debug_stream << v4 << '\n'; // [C,A,G,T,G,A,C,T,A]
}

This entity is stable. Since version 3.1.

◆ to_rank

auto const seqan3::views::to_rank

inline

A view that calls seqan3::to_rank() on each element in the input range.

Template Parameters

urng_t The type of the range being processed. See below for requirements. [template parameter is omitted in pipe notation]

Parameters

[in] urange The range being processed. [parameter is omitted in pipe notation]

Returns: A range of converted elements. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/to_rank.hpp>

View properties

This view is a deep view Given a range-of-range as input (as opposed to just a range), it will apply the transformation on the innermost range (instead of the outermost range).

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range		preserved
std::ranges::bidirectional_range		preserved
std::ranges::random_access_range		preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range		preserved
std::ranges::common_range		preserved
std::ranges::output_range		lost
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::alphabet	seqan3::alphabet_rank_t<std::ranges::range_value_t<urng_t>>

See the views submodule documentation for detailed descriptions of the view properties.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/quality/aliases.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/views/to_rank.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna4_vector vec = "ACTTTGATA"_dna4;
    auto v = vec | seqan3::views::to_rank;
    seqan3::debug_stream << v << '\n'; // [0,1,3,3,3,2,0,3,0]
 
    std::vector<seqan3::phred42> qvec{seqan3::phred42{}.assign_phred(0),
                                      seqan3::phred42{}.assign_phred(7),
                                      seqan3::phred42{}.assign_phred(5),
                                      seqan3::phred42{}.assign_phred(3),
                                      seqan3::phred42{}.assign_phred(7),
                                      seqan3::phred42{}.assign_phred(4),
                                      seqan3::phred42{}.assign_phred(30),
                                      seqan3::phred42{}.assign_phred(16),
                                      seqan3::phred42{}.assign_phred(23)};
 
    auto v3 = qvec | seqan3::views::to_rank;
    seqan3::debug_stream << v3 << '\n'; // [0,7,5,3,7,4,30,16,23]
 
    std::vector<seqan3::dna4q> qcvec{{'C'_dna4, '!'_phred42},
                                     {'A'_dna4, '('_phred42},
                                     {'G'_dna4, '&'_phred42},
                                     {'T'_dna4, '$'_phred42},
                                     {'G'_dna4, '('_phred42},
                                     {'A'_dna4, '%'_phred42},
                                     {'C'_dna4, '?'_phred42},
                                     {'T'_dna4, '1'_phred42},
                                     {'A'_dna4, '8'_phred42}};
    auto v4 = qcvec | seqan3::views::to_rank;
    seqan3::debug_stream << v4 << '\n'; // [42,7,89,129,91,4,72,142,23]
}

We also convert to unsigned here, because the seqan3::alphabet_rank_t is often uint8_t which is often implemented as unsigned char and thus will not be printed as a number by default.

This entity is stable. Since version 3.1.

◆ translate

constexpr auto seqan3::views::translate

inlineconstexpr

A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames.

Template Parameters

urng_t The type of the range being processed.

Parameters

[in]	urange	The range being processed.
[in]	tf	A value of seqan3::tanslation_frames that indicates the desired frames.

Returns: A range of ranges containing frames with aminoacid sequence. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/translate.hpp>

This view can be used to translate nucleotide sequences into aminoacid sequences (see translation_frames for possible combination of frames).

View properties

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range	required	preserved
std::ranges::bidirectional_range	required	preserved
std::ranges::random_access_range	required	preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range	required	preserved
std::ranges::common_range		guaranteed
std::ranges::output_range		lost
seqan3::const_iterable_range	required	preserved

std::ranges::range_reference_t	seqan3::nucleotide_alphabet	std::ranges::view && std::ranges::random_access_range && std::ranges::sized_range

urng_t is the type of the range modified by this view (input).
rrng_type is the type of the range returned by this view.
for more details, see views.

Example

Operating on a range of seqan3::dna5:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/views/complement.hpp>
#include <seqan3/alphabet/views/translate.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna5_vector vec{"ACGTACGTACGTA"_dna5};
 
    // default frame translation
    auto v1 = vec | seqan3::views::translate;
    seqan3::debug_stream << v1 << '\n'; // [TYVR,RTYV,VRT,YVRT,TYVR,RTY]
 
    // single frame translation
    auto v2 = vec | seqan3::views::translate(seqan3::translation_frames::forward_frame0);
    seqan3::debug_stream << v2 << '\n'; // [TYVR]
 
    // reverse translation
    auto v3 = vec | seqan3::views::translate(seqan3::translation_frames::forward_reverse0);
    seqan3::debug_stream << v3 << '\n'; // [TYVR,YVRT]
 
    // forward frames translation
    auto v4 = vec | seqan3::views::translate(seqan3::translation_frames::forward_frames);
    seqan3::debug_stream << v4 << '\n'; // [TYVR,RTYV,VRT]
 
    // six frame translation
    auto v5 = vec | seqan3::views::translate(seqan3::translation_frames::six_frames);
    seqan3::debug_stream << v5 << '\n'; // [TYVR,RTYV,VRT,YVRT,TYVR,RTY]
 
    // function syntax
    auto v6 = seqan3::views::translate(vec, seqan3::translation_frames::forward_reverse0);
    seqan3::debug_stream << v6 << '\n'; // [TYVR,YVRT]
 
    // combinability
    auto v7 = vec | seqan3::views::complement | seqan3::views::translate(seqan3::translation_frames::forward_reverse0);
    seqan3::debug_stream << v7 << '\n'; // [CMHA,MHAC]
}

See also: seqan3::translate_triplet; seqan3::views::translate_single; seqan3::views::translate_join

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ translate_join

constexpr auto seqan3::views::translate_join

inlineconstexpr

A view that translates nucleotide into aminoacid alphabet with 1, 2, 3 or 6 frames. Input and output range are always two-dimensional.

Template Parameters

urng_t The type of the range being processed.

Parameters

[in]	urange	The range being processed. Needs to be a range of ranges (two-dimensional).
[in]	tf	A value of seqan3::tanslation_frames that indicates the desired frames.

Returns: A range of ranges containing frames with aminoacid sequence. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/translate_join.hpp>

This view can be used to translate nucleotide sequences into aminoacid sequences (see translation_frames for possible combination of frames). This view only operates on two-dimensional input (range of ranges) and outputs a range of ranges no matter the number of input sequences or the number of translation frames given. Therefore, it has the same capabilities as the standard view_translate but concatenates the different frames of the different input sequences rather than having a separate range for each input sequence containing the translated frames. In the output, frames are ordered in a way, that all requested frames are listed per sequence directly after each other in the order of input sequences. improved and efficient downstream post-processing if needed. However, the index of a frame for a specific sequence needs to be calculated via modulo operations in this case. The i-th frame of the j-th sequence can be calculated by n = (i * s) + j, where s is the number of frames used for translation (index starting at zero).

In short, this views behaves the same as:

std::vector<std::vector<dna5>> vec {...};

auto v = vec | views::translate | std::views::join;

Except that the performance is better and the returned range still models std::ranges::random_access_range and std::ranges::sized_range.

View properties

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range	required	preserved
std::ranges::bidirectional_range	required	preserved
std::ranges::random_access_range	required	preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range	required	preserved
std::ranges::common_range		guaranteed
std::ranges::output_range		lost
seqan3::const_iterable_range	required	preserved

std::ranges::range_reference_t	seqan3::nucleotide_alphabet	std::ranges::view && std::ranges::random_access_range && std::ranges::sized_range

urng_t is the type of the range modified by this view (input).
rrng_t is the type of the range returned by this view.
for more details, see views.

Example

Operating on a range of seqan3::dna5:

#include <iostream>
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/views/char_to.hpp>
#include <seqan3/alphabet/views/translate_join.hpp>
#include <seqan3/core/debug_stream.hpp>
 
using namespace seqan3::literals;
 
int main()
{
    // Input range needs to be two-dimensional
    std::vector<std::vector<seqan3::dna4>> vec{"ACGTACGTACGTA"_dna4, "TCGAGAGCTTTAGC"_dna4};
 
    // Translation with default parameters
    auto v1 = vec | seqan3::views::translate_join;
    seqan3::debug_stream << v1 << "\n"; // [TYVR,RTYV,VRT,YVRT,TYVR,RTY,SRAL,REL*,ESFS,AKAL,LKLS,*SSR]
 
    // Access the third forward frame (index_frame 2) of the second input sequence (index_seq 1)
    // Required frames per sequence s = 6
    // n = (index_seq * s) + j
    //   = 1 * 6 + 2
    //   = 8
 
    auto third_frame_second_seq = v1[1 * 6 + 2];
    seqan3::debug_stream << third_frame_second_seq << "\n"; // ESFS
 
    // Translation with custom translation frame
    auto v2 = vec | seqan3::views::translate_join(seqan3::translation_frames::forward_frame0);
    seqan3::debug_stream << v2 << "\n"; // [TYVR,SRAL]
 
    return 0;
}

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ translate_single

constexpr auto seqan3::views::translate_single

inlineconstexpr

A view that translates nucleotide into aminoacid alphabet for one of the six frames.

Template Parameters

urng_t The type of the range being processed.

Parameters

[in]	urange	The range being processed.
[in]	tf	A value of seqan3::translation_frames that indicates the desired frames.

Returns: A range containing frames with aminoacid sequence. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/translate.hpp>

This view can be used to translate nucleotide sequences into aminoacid sequences (see translation_frames for possible combination of frames).

View properties

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range	required	preserved
std::ranges::bidirectional_range	required	preserved
std::ranges::random_access_range	required	preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range	required	preserved
std::ranges::common_range		guaranteed
std::ranges::output_range		lost
seqan3::const_iterable_range	required	preserved

std::ranges::range_reference_t	seqan3::nucleotide_alphabet	seqan3::aa27

urng_t is the type of the range modified by this view (input).
rrng_type is the type of the range returned by this view.
for more details, see views.

Example

Operating on a range of seqan3::dna5:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/views/complement.hpp>
#include <seqan3/alphabet/views/translate.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna5_vector vec{"ACGTACGTACGTA"_dna5};
 
    // Default (first forward frame)
    auto v1 = vec | seqan3::views::translate_single;
    // == [T,Y,V,R]
    seqan3::debug_stream << v1[1] << '\n';
 
    // First forward frame
    auto v2 = vec | seqan3::views::translate_single(seqan3::translation_frames::forward_frame0);
    // == [T,Y,V,R]
 
    // First reverse frame
    auto v3 = vec | seqan3::views::translate_single(seqan3::translation_frames::reverse_frame0);
    // == [Y,V,R,T]
 
    // Second forward frame
    auto v4 = vec | seqan3::views::translate_single(seqan3::translation_frames::forward_frame1);
    // == [R,T,Y,V]
 
    // Second reverse frame
    auto v5 = vec | seqan3::views::translate_single(seqan3::translation_frames::reverse_frame1);
    // == [T,Y,V,R]
 
    // Third forward frame
    auto v6 = vec | seqan3::views::translate_single(seqan3::translation_frames::forward_frame2);
    // == [V,R,T]
 
    // Third reverse frame
    auto v7 = vec | seqan3::views::translate_single(seqan3::translation_frames::reverse_frame2);
    // == [R,T,Y]
 
    // function syntax
    auto v8 = seqan3::views::translate_single(vec, seqan3::translation_frames::forward_frame0);
    // == [T,Y,V,R]
 
    // combinability
    auto v9 =
        vec | seqan3::views::complement | seqan3::views::translate_single(seqan3::translation_frames::reverse_frame0);
    // == [M,H,A,C]
 
    // combinability with default parameter
    auto v10 = vec | seqan3::views::complement | seqan3::views::translate_single;
    // == [C,M,H,A]
 
    // combinability with default parameter
    auto v11 = vec | seqan3::views::complement | seqan3::views::translate_single();
    // == [C,M,H,A]
}

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ trim_quality

constexpr auto seqan3::views::trim_quality

inlineconstexpr

A view that does quality-threshold trimming on a range of seqan3::quality_alphabet.

Template Parameters

urng_t	The type of the range being processed. See below for requirements.
threshold_t	Either std::ranges::range_value_t<urng_t> or seqan3::alphabet_phred_t<std::ranges::range_value_t<urng_t>>.

Parameters

[in]	urange	The range being processed. [parameter is omitted in pipe notation]
[in]	threshold	The minimum quality.

Returns: A trimmed range. See below for the properties of the returned range.

Header File

#include <seqan3/alphabet/views/trim_quality.hpp>

This view can be used to trim sequences based on quality. Only bases at the end of the sequence not meeting the specified threshold are discarded.

View properties

This view is a deep view Given a range-of-range as input (as opposed to just a range), it will apply the transformation on the innermost range (instead of the outermost range).

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range		preserved
std::ranges::bidirectional_range		preserved
std::ranges::random_access_range		preserved

std::ranges::view		guaranteed
std::ranges::sized_range		lost
std::ranges::common_range		lost
std::ranges::output_range		preserved
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::quality_alphabet	std::ranges::range_reference_t<urng_t>

See the views submodule documentation for detailed descriptions of the view properties.

Example

Operating on a range of seqan3::phred42:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <string>
#include <vector>
 
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/views/to_char.hpp>
#include <seqan3/alphabet/views/trim_quality.hpp>
#include <seqan3/core/debug_stream.hpp>
 
using namespace seqan3::literals;
 
int main()
{
    std::vector<seqan3::phred42> vec{"II?5+"_phred42};
 
    // trim by phred_value
    auto v1 = vec | seqan3::views::trim_quality(20u);
    seqan3::debug_stream << v1 << '\n'; // II?5
 
    // trim by quality character
    auto v2 = vec | seqan3::views::trim_quality('I'_phred42);
    seqan3::debug_stream << v2 << '\n'; // II
 
    // function syntax
    auto v3 = seqan3::views::trim_quality(vec, '5'_phred42);
    seqan3::debug_stream << v3 << '\n'; // II?5
 
    // combinability
    auto v4 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char;
    seqan3::debug_stream << v4 << '\n'; // II?5
}

Or operating on a range of seqan3::dna5q:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <string>
#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/quality/aliases.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/views/to_char.hpp>
#include <seqan3/alphabet/views/trim_quality.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    std::vector<seqan3::dna5q> vec{{'A'_dna5, 'I'_phred42},
                                   {'G'_dna5, 'I'_phred42},
                                   {'G'_dna5, '?'_phred42},
                                   {'A'_dna5, '5'_phred42},
                                   {'T'_dna5, '+'_phred42}};
 
    // trim by phred_value
    auto v1 = vec | seqan3::views::trim_quality(20u);
    seqan3::debug_stream << v1 << '\n'; // AGGA
 
    // trim by quality character; in this case the nucleotide part of the character is irrelevant
    auto v2 = vec | seqan3::views::trim_quality(seqan3::dna5q{'C'_dna5, '5'_phred42});
    seqan3::debug_stream << v2 << '\n'; // AGGA
 
    // combinability
    auto v3 = seqan3::views::trim_quality(vec, 20u) | seqan3::views::to_char;
    seqan3::debug_stream << v3 << '\n'; // AGGA
}

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ validate_char_for

template<alphabet alphabet_type>

auto const seqan3::views::validate_char_for

inline

An identity view that throws if an encountered character is not valid for the given alphabet.

Template Parameters

urng_t	The type of the range being processed. See below for requirements. [template parameter is omitted in pipe notation]
alphabet_t	The alphabet to check validity for; must satisfy seqan3::alphabet.

Parameters

[in] urange The range being processed. [parameter is omitted in pipe notation]

Returns: The range of input values. See below for the properties of the returned range.

Exceptions

seqan3::invalid_char_assignment if an invalid character is encountered.

Header File

#include <seqan3/alphabet/views/validate_char_for.hpp>

This view throws if it encounters a character that is not in the valid set of an alphabet. It performs no transformation on the elements of the view itself. However, the contiguous property is lost due to the way it is currently implemented.

View properties

This view is a deep view. Given a range-of-range as input (as opposed to just a range), it will apply the transformation on the innermost range (instead of the outermost range).

Concepts and traits	`urng_t` (underlying range type)	`rrng_t` (returned range type)
std::ranges::input_range	required	preserved
std::ranges::forward_range		preserved
std::ranges::bidirectional_range		preserved
std::ranges::random_access_range		preserved
std::ranges::contiguous_range		lost

std::ranges::viewable_range	required	guaranteed
std::ranges::view		guaranteed
std::ranges::sized_range		preserved
std::ranges::common_range		preserved
std::ranges::output_range		preserved
std::semiregular		preserved
seqan3::const_iterable_range		preserved

std::ranges::range_reference_t	seqan3::alphabet_char_t<alphabet_t>	std::ranges::range_reference_t<urng_t>

See the views submodule documentation for detailed descriptions of the view properties.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/views/validate_char_for.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    std::string_view str{"ACTTTGATAN"};
    try
    {
        seqan3::debug_stream << (str | seqan3::views::validate_char_for<seqan3::dna4>); // ACTTTGATA
    }
    catch (seqan3::invalid_char_assignment const &)
    {
        seqan3::debug_stream << "\n[ERROR] Invalid char!\n"; // Will throw on parsing 'N'
    }
}

This entity is experimental and subject to change in the future. Experimental since version 3.2.

Variables

Alphabet related views

Detailed Description

Variable Documentation

◆ char_strictly_to

View properties

Example

◆ char_to

View properties

Example

◆ complement

View properties

Example

◆ minimiser_hash

Non-lexicographical Minimisers by skewing the hash value with a seed

View properties

Example

◆ rank_to

View properties

Example

◆ to_char

View properties

Example

◆ to_rank

View properties

Example

◆ translate

View properties

Example

◆ translate_join

View properties

Example

◆ translate_single

View properties

Example

◆ trim_quality

View properties

Example

◆ validate_char_for

View properties

Example