| Safe Haskell | None |
|---|---|
| Language | Haskell2010 |
Biobase.Primary.Nuc
Description
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
Synopsis
- module Biobase.Primary.Letter
- module Biobase.Primary.Nuc.Conversion
- acgt :: [Letter DNA n]
- charDNA :: Char -> Letter DNA n
- dnaChar :: Letter DNA n -> Char
- cdna :: Iso' Char (Letter DNA n)
- dnaSeq :: MkPrimary p DNA n => p -> Primary DNA n
- acgu :: [Letter RNA n]
- charRNA :: Char -> Letter RNA n
- rnaChar :: Letter RNA n -> Char
- crna :: Iso' Char (Letter RNA n)
- rnaSeq :: MkPrimary p RNA n => p -> Primary RNA n
- charXNA :: Char -> Letter XNA n
- xnaChar :: Letter XNA n -> Char
- xnaSeq :: MkPrimary p XNA n => p -> Primary XNA n
Documentation
module Biobase.Primary.Letter
cdna :: Iso' Char (Letter DNA n) Source #
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.