Biobase.Secondary.Basepair

Secondary structure: define basepairs as Int-tuples, the three edges, a nucleotide can use for pairing and the cis/trans isomerism. Both edges and cis/trans come with a tag for "unknown".

TODO set ext-annotations to be (isomerism,edge,edge) and have a asString instance to read "cWW" "tSH" and other notation.

Newtypes for extended secondary structures

Encode which of three edges is engaged in base pairing

newtype Edge

Each nucleotide in a pair may be paired using one of three edges: watson-crick, sugar, or hoogsteen.

Constructors

Edge

Fields

unEdge :: Int

Instances

Bounded Edge

Enum Edge

Eq Edge

Ord Edge

Read Edge

Human-readable Read instance.

Show Edge

Human-readable Show instance.

Ix Edge

Generic Edge

ToJSON Edge

FromJSON Edge

Binary Edge

Serialize Edge

Unbox Edge

IsostericityLookup ExtPair

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

TODO inClass missing

Vector Vector Edge

MVector MVector Edge

RemovePseudoKnots [ExtPairIdx]

RemovePseudoKnots (Vector ExtPairIdx)

Remove pseudoknotted pairs from extended RNA secondary structures.

MkD2Secondary (Int, [ExtPairIdx])

BaseSelect ((a, a), ExtPairAnnotation) a

extended pairtype annotation given

type Rep Edge

data Vector Edge = V_Edge (Vector Int)

data MVector s0 Edge = MV_Edge (MVector s Int)

pattern W :: Edge

pattern S :: Edge

pattern H :: Edge

Is the base pair in cis or trans configuration

newtype CTisomerism

Nucleotides in a pairing may be in the cis(==?) or trans(==?) state.

Constructors

CT

Fields

unCT :: Int

Instances

Bounded CTisomerism

Enum CTisomerism

Eq CTisomerism

Ord CTisomerism

Read CTisomerism

Human-readable Read instance.

Show CTisomerism

Human-readable Show instance.

Ix CTisomerism

Generic CTisomerism

ToJSON CTisomerism

FromJSON CTisomerism

Binary CTisomerism

Serialize CTisomerism

Unbox CTisomerism

IsostericityLookup ExtPair

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

TODO inClass missing

Vector Vector CTisomerism

MVector MVector CTisomerism

RemovePseudoKnots [ExtPairIdx]

RemovePseudoKnots (Vector ExtPairIdx)

Remove pseudoknotted pairs from extended RNA secondary structures.

MkD2Secondary (Int, [ExtPairIdx])

BaseSelect ((a, a), ExtPairAnnotation) a

extended pairtype annotation given

type Rep CTisomerism

data Vector CTisomerism = V_CTisomerism (Vector Int)

data MVector s0 CTisomerism = MV_CTisomerism (MVector s Int)

pattern Cis :: CTisomerism

pattern Trn :: CTisomerism

Types

type PairIdx = (Int, Int)

A basepair is simply a pair of Ints which are 0-indexing a sequence.

type Pair = (Letter RNA, Letter RNA)

A pair as a tuple containing Nucs.

type ExtPairAnnotation = (CTisomerism, Edge, Edge)

Annotation for a basepair.

type ExtPairIdx = (PairIdx, ExtPairAnnotation)

An extended basepair is a basepair, annotated with edge and CTisomerism.

type ExtPair = (Pair, ExtPairAnnotation)

An extended basepair, with nucleotides an annotation.

little helpers

pattern CHH :: (CTisomerism, Edge, Edge)

pattern CHS :: (CTisomerism, Edge, Edge)

pattern CHW :: (CTisomerism, Edge, Edge)

pattern CSH :: (CTisomerism, Edge, Edge)

pattern CSS :: (CTisomerism, Edge, Edge)

pattern CSW :: (CTisomerism, Edge, Edge)

pattern CWH :: (CTisomerism, Edge, Edge)

pattern CWS :: (CTisomerism, Edge, Edge)

pattern CWW :: (CTisomerism, Edge, Edge)

pattern THH :: (CTisomerism, Edge, Edge)

pattern THS :: (CTisomerism, Edge, Edge)

pattern THW :: (CTisomerism, Edge, Edge)

pattern TSH :: (CTisomerism, Edge, Edge)

pattern TSS :: (CTisomerism, Edge, Edge)

pattern TSW :: (CTisomerism, Edge, Edge)

pattern TWH :: (CTisomerism, Edge, Edge)

pattern TWS :: (CTisomerism, Edge, Edge)

pattern TWW :: (CTisomerism, Edge, Edge)

tuple-like selection

class BaseSelect a b | a -> b where

Selection of nucleotides and/or type classes independent of which type we are looking at.

Methods

baseL :: a -> b

select first index or nucleotide

baseR :: a -> b

select second index or nucleotide

baseP :: a -> (b, b)

select both nucleotides as pair

baseT :: a -> ExtPairAnnotation

select basepair type if existing or return default cWW

updL :: b -> a -> a

update first index or nucleotide

updR :: b -> a -> a

update second index or nucleotide

updP :: (b, b) -> a -> a

update complete pair

updT :: ExtPairAnnotation -> a -> a

update basepair type, error if not possible due to type a

Instances

BaseSelect ((a, a), ExtPairAnnotation) a

extended pairtype annotation given

BaseSelect (a, a) a

simple cis/wc-wc basepairs