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Merge pull request #1191 from sarahet/add_dna3bs_alphabet
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[Feature] Add dna3bs alphabet
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@h-2
h-2 authored Jul 29, 2019
2 parents 28714c7 + e6a2bd6 commit a60194e
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44 changes: 25 additions & 19 deletions include/seqan3/alphabet/nucleotide/all.hpp
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#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/dna3bs.hpp>
#include <seqan3/alphabet/nucleotide/rna4.hpp>
#include <seqan3/alphabet/nucleotide/rna5.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
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* to represent them in a regular std::string, it makes sense to have specialised data structures in most cases.
* This sub-module offers multiple nucleotide alphabets that can be used with regular containers and ranges.
*
* | Letter | Description | seqan3::dna15 | seqan3::dna5 | seqan3::dna4 | seqan3::rna15 | seqan3::rna5 | seqan3::rna4 |
* |:--------:|------------------------|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|
* | A | Adenine | A | A | A | A | A | A |
* | C | Cytosine | C | C | C | C | C | C |
* | G | Guanine | G | G | G | G | G | G |
* | T | Thymine (DNA) | T | T | T | <span style="color:LightGrey">U</span> | <span style="color:LightGrey">U</span> | <span style="color:LightGrey">U</span> |
* | U | Uracil (RNA) | <span style="color:LightGrey">T</span> | <span style="color:LightGrey">T</span> | <span style="color:LightGrey">T</span> | U | U | U |
* | M | A *or* C | M | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | M | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | R | A *or* G | R | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | R | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | W | A *or* T | W | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | W | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | Y | C *or* T | Y | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> | Y | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> |
* | S | C *or* G | S | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> | S | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> |
* | K | G *or* T | K | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">G</span> | K | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">G</span> |
* | V | A *or* C *or* G | V | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | V | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | H | A *or* C *or* T | H | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | H | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | D | A *or* G *or* T | D | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | D | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | B | C *or* G *or* T | B | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> | B | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> |
* | N | A *or* C *or* G *or* T | N | N | <span style="color:LightGrey">A</span> | N | N | <span style="color:LightGrey">A</span> |
* | **Size** | | 15 | 5 | 4 | 15 | 5 | 4 |
* | Letter | Description | seqan3::dna15 | seqan3::dna5 | seqan3::dna4 | seqan3::dna3bs | seqan3::rna15 | seqan3::rna5 | seqan3::rna4 |
* |:--------:|------------------------|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|:--------------------------------------:|
* | A | Adenine | A | A | A | A | A | A | A |
* | C | Cytosine | C | C | C | T | C | C | C |
* | G | Guanine | G | G | G | G | G | G | G |
* | T | Thymine (DNA) | T | T | T | T | <span style="color:LightGrey">U</span> | <span style="color:LightGrey">U</span> | <span style="color:LightGrey">U</span> |
* | U | Uracil (RNA) | <span style="color:LightGrey">T</span> | <span style="color:LightGrey">T</span> | <span style="color:LightGrey">T</span> | <span style="color:LightGrey">T</span> | U | U | U |
* | M | A *or* C | M | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | <span style="color:LightGrey">A</span> | M | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | R | A *or* G | R | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | <span style="color:LightGrey">A</span> | R | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | W | A *or* T | W | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | <span style="color:LightGrey">A</span> | W | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | Y | C *or* T | Y | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">T</span> | <span style="color:LightGrey">C</span> | Y | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> |
* | S | C *or* G | S | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">T</span> | <span style="color:LightGrey">C</span> | S | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> |
* | K | G *or* T | K | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">G</span> | <span style="color:LightGrey">G</span> | K | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">G</span> |
* | V | A *or* C *or* G | V | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | <span style="color:LightGrey">A</span> | V | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | H | A *or* C *or* T | H | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | <span style="color:LightGrey">A</span> | H | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | D | A *or* G *or* T | D | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> | <span style="color:LightGrey">A</span> | D | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">A</span> |
* | B | C *or* G *or* T | B | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">T</span> | <span style="color:LightGrey">C</span> | B | <span style="color:LightGrey">N</span> | <span style="color:LightGrey">C</span> |
* | N | A *or* C *or* G *or* T | N | N | <span style="color:LightGrey">A</span> | <span style="color:LightGrey">A</span> | N | N | <span style="color:LightGrey">A</span> |
* | **Size** | | 15 | 5 | 3 | 4 | 15 | 5 | 4 |
*
* Keep in mind, that while we think of "the nucleotide alphabet" as consisting of four bases, there are indeed
* more characters defined with different levels of ambiguity. Depending on your application it will make sense
Expand All @@ -67,6 +68,7 @@
* 4. if you are doing only RNA input/output, use the respective seqan3::rna* type
* 5. to actually save space from using smaller alphabets, you need a compressed container (e.g.
* seqan3::bitcompressed_vector)
* 6. if you are working with bisulfite data use seqan3::dna3bs
*
* ###Printing and conversion to char
*
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* pairs with. To generate the complement value of a nucleotide letter, you can call an implementation of
* seqan3::NucleotideAlphabet::complement() on it.
*
* The only exception to this table is the seqan3::dna3bs alphabet. The complement for 'G' is defined as 'T' since 'C' and 'T'
* are treated as the same letters. However, it is not recommended to use the complement of seqan3::dna3bs but rather
* use the complement of another dna alphabet and afterwards transform it into seqan3::dna3bs.
*
* For the ambiguous letters, the complement is the (possibly also ambiguous) letter representing the variant of the
* individual complements.
*
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