Biobase.Primary

The primary structure: interface to efficient encoding of RNA and DNA sequences. The design aims toward the vector library and repa. In particular, everything is strict; if you want to stream full genomes, use text or lazy bytestrings instead and cast to Biobase.Primary definitions only at the last moment.

NOTE individual nucleotides are encoded is Ints internally without any tagging. This means that we have no way of deciding if we are dealing with RNA or DNA on this level.

Convert different types of sequence representations to the internal

class MkPrimary a where

Given a sequence of nucleotides encoded in some text-form, create a Nuc-based unboxed vector.

Methods

mkPrimary :: a -> Primary

Instances

MkPrimary String

MkPrimary ByteString

MkPrimary ByteString

MkPrimary Text

MkPrimary [Nuc]

type Primary = Vector Nuc

Efficient nucleotide encoding

newtype Nuc

Constructors

Nuc

Fields

unNuc :: Int

Instances

Bounded Nuc

The bounded instance from GHC proper. Captures all defined symbols.

Enum Nuc

Enum

Eq Nuc

Ord Nuc

Read Nuc

Human-readable Read instance.

Show Nuc

Human-readable Show instance.

Ix Nuc

Prim Nuc

Unbox Nuc

Bounds Nuc

Special bounds for energy / score arrays

IsostericityLookup ExtPair

For extended basepairs, we take the default mapping and go from there.

TODO inClass missing

IsostericityLookup Pair

Normal basepairs are assumed to have cWW basepairing.

TODO inClass missing

Vector Vector Nuc

MVector MVector Nuc

MkPrimary [Nuc]

(Shape sh, Show sh) => Shape (:. sh Nuc)

MkViennaPair (Nuc, Nuc)

mkNuc :: Char -> Nuc

Translate between Chars and Nucs.

fromNuc :: Nuc -> Char

Instances of different type classes

instances for Nuc

Instances for MkPrimary