class for nucleotides

[Peter]

I need some utilities for dealing with sequences of nucleotides both DNA and RNA. DNA and RNA should be supported in two different classes (possibly inherited or encapsulating shared functionality in a member variable). Typically a DNA is represented by A,C,G, and T, but I'd like support also for

N = any
R = A | G
W = A | T
Y = C | T
M = A | C
K = G | T
S = G | C
H = !G
B = !A
V = !T
D = !C

Support for translating RNA->DNA and DNA->RNA.

Comparison operators

For equality, most important to compare in such a way that equal means: could be equal i.e. 'N'=='A', 'S'=='G', but 'S'!='A'. When it comes to LessThanComparison it is not obvious how to define it so it is in line with equality definition and also fulfills ​Strict Weak Ordering.

Sequance

When it comes to the sequence i.e. an array of nucleotides either a std::vector could be used, or a wrapper class around vector, or possibly string_stream<T> (??).

Iterators are essential (to enable std::algorithm). Both normal and reverse iterators, as well as complement and reverse_complement should be supported. The latter pair of iterators transform according to WC-pairing such that A becomes T, and C becomes G, and vice versa. Complement iterators should probably only support const iterator, since a mutable transform iterator is a bit tricky (when they appear as on LHS in assignment).

[Peter]

It is not possible to define LessThanComparison obeying Strict Weak Ordering when having those fuzzy nucleotides. The reason is easiest illustrated by N which should be equivalent with any other nucleotide. However, Strict Weak Ordering requires that

If x and y are equivalent as well as x and z, then it follows that y and z are equivalent.

Replacing x with N, obviously anything would become equivalent with anything, in other words, operator< would return false all the time, pretty meaningless.

[Jari Häkkinen]

How about sequence of amino acids?

[Peter]

I have a DNA class declared as follows:

class DNA : boost::operators<DNA>
{
public:
	DNA(void);
	DNA(char);
	DNA complement(void) const;
	char get(void) const;
	DNA& operator&=(const DNA& other);
	DNA& operator|=(const DNA& other);
	DNA& operator^=(const DNA& other);
};  
bool operator==(const DNA& lhs, const DNA& rhs);
std::ostream& operator<<(std::ostream&, const DNA&);

The behavior is a not exacly the same as described above, but is there any interest for such a class?

[Jari Häkkinen]

Replying to peter:

The behavior is a not exacly the same as described above, but is there any interest for such a class?

I will probably become interested after the summer so please add it.

[Peter]

which namespace? utility?

[Jari Häkkinen]

Replying to peter:

which namespace? utility?

Sure. If we find a better namespace later we can moved (prior to 1.0 ;-) )

[Peter]

I think I put this in a new namespace omic together with a small class for GenomicPosition.

[Peter]

(In [2341]) New namespace omic and new class omic::DNA. closes #377

[Peter]

(In [2342]) adding missing files. refs #377

[Peter]

(In [2343]) adding missing file. refs #377