Biobase.Primary.Nuc

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.

Degenerate encoding can be found in the IUPAC module.

TODO enable OverloadedLists

Documentation

module Biobase.Primary.Letter

module Biobase.Primary.Nuc.Conversion

acgt :: [Letter DNA n]

charDNA :: forall k (n :: k). Char -> Letter DNA n

dnaChar :: forall k (n :: k). Letter DNA n -> Char

cdna :: Iso' Char (Letter DNA n)

An isomorphism from Char to 'Letter DNA'. This assumes that the underlying Chars actually represent a DNA sequence. This allows typesafe modification of DNA sequences since only [A,C,G,T,N] are allowed.

dnaSeq :: MkPrimary p DNA n => p -> Primary DNA n

acgu :: [Letter RNA n]

charRNA :: forall k (n :: k). Char -> Letter RNA n

rnaChar :: forall k (n :: k). Letter RNA n -> Char

crna :: Iso' Char (Letter RNA n)

An isomorphism from Char to 'Letter RNA'. This assumes that the underlying Chars actually represent an RNA sequence. This allows typesafe modification of RNA sequences since only [A,C,G,U,N] are allowed.

rnaSeq :: MkPrimary p RNA n => p -> Primary RNA n

viennaPairs :: forall k1 k2 (n1 :: k1) (n2 :: k2). [(Letter RNA n1, Letter RNA n2)]

viennaPairsNN :: forall k1 k2 (n1 :: k1) (n2 :: k2). [(Letter RNA n1, Letter RNA n2)]

charXNA :: forall k (n :: k). Char -> Letter XNA n

xnaChar :: forall k (n :: k). Letter XNA n -> Char

xnaSeq :: MkPrimary p XNA n => p -> Primary XNA n