Safe Haskell	None
Language	Haskell2010

Biobase.Primary.IUPAC

Contents

Conversions
Raw embeddings

Description

Degenerate base symbol representation. We use the same conventions as in which ignores Uracil, except if it stands alone for Char and XNA targets. If the Degenerate target is RNA, then we create Us instead of Ts.

TODO Shall we handle Complement for degenerates?

Synopsis

Documentation

data DEG Source

Allow the full, including degenerates, alphabet.

Instances

Bounded (Letter DEG)
Enum (Letter DEG)
Show (Letter DEG)
IsString [Letter DEG]
MkPrimary (Vector Char) DEG

pattern A :: Letter DEG Source

pattern C :: Letter DEG Source

pattern G :: Letter DEG Source

pattern T :: Letter DEG Source

pattern U :: Letter DEG Source

pattern W :: Letter DEG Source

pattern S :: Letter DEG Source

pattern M :: Letter DEG Source

pattern K :: Letter DEG Source

pattern R :: Letter DEG Source

pattern Y :: Letter DEG Source

pattern B :: Letter DEG Source

pattern D :: Letter DEG Source

pattern H :: Letter DEG Source

pattern V :: Letter DEG Source

pattern N :: Letter DEG Source

charDEG :: Char -> Letter DEG Source

degChar :: Letter DEG -> Char Source

degSeq :: MkPrimary n DEG => n -> Primary DEG Source

Conversions

class Degenerate x where Source

Methods

fromDegenerate :: Char -> [x] Source

toDegenerate :: [x] -> Maybe Char Source

Instances

Degenerate Char
Degenerate (Letter RNA)
Degenerate (Letter DNA)
Degenerate (Letter XNA)

Raw embeddings

iupacXDNAchars :: [(Char, String)] Source

list of characters, using the XNA alphabet, but degenerate chars assume DNA characters.

iupacNucleotides :: ByteString Source

Raw iupac data, embedded into the library.