Safe Haskell | None |
---|---|
Language | Haskell2010 |
Degenerate base symbol representation. We use the same conventions as in
which ignores
U
racil, except if it stands alone for Char
and XNA
targets. If the
Degenerate
target is RNA
, then we create U
s instead of T
s.
TODO Shall we handle Complement
for degenerates?
- data DEG
- pattern A :: Letter DEG
- pattern C :: Letter DEG
- pattern G :: Letter DEG
- pattern T :: Letter DEG
- pattern U :: Letter DEG
- pattern W :: Letter DEG
- pattern S :: Letter DEG
- pattern M :: Letter DEG
- pattern K :: Letter DEG
- pattern R :: Letter DEG
- pattern Y :: Letter DEG
- pattern B :: Letter DEG
- pattern D :: Letter DEG
- pattern H :: Letter DEG
- pattern V :: Letter DEG
- pattern N :: Letter DEG
- charDEG :: Char -> Letter DEG
- degChar :: Letter DEG -> Char
- degSeq :: MkPrimary n DEG => n -> Primary DEG
- class Degenerate x where
- fromDegenerate :: Char -> [x]
- toDegenerate :: [x] -> Maybe Char
- iupacXDNAchars :: [(Char, String)]
- iupacNucleotides :: ByteString
Documentation
Allow the full, including degenerates, alphabet.
Conversions
class Degenerate x where Source
fromDegenerate :: Char -> [x] Source
toDegenerate :: [x] -> Maybe Char Source
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.