Bio.Seq

Alphabet

data Basic

Alphabet defined by http://www.chem.qmul.ac.uk/iupac/ | Standard unambiguous alphabet

Instances

BioSeq RNA Basic

Methods

alphabet :: Proxy * (RNA Basic) -> HashSet Char

fromBS :: ByteString -> Either String (RNA Basic)

BioSeq DNA Basic

Methods

alphabet :: Proxy * (DNA Basic) -> HashSet Char

fromBS :: ByteString -> Either String (DNA Basic)

data IUPAC

full IUPAC alphabet, including ambiguous letters

Instances

BioSeq DNA IUPAC

Methods

alphabet :: Proxy * (DNA IUPAC) -> HashSet Char

fromBS :: ByteString -> Either String (DNA IUPAC)

data Ext

extended alphabet

Instances

BioSeq DNA Ext

Methods

alphabet :: Proxy * (DNA Ext) -> HashSet Char

fromBS :: ByteString -> Either String (DNA Ext)

Sequence types

data DNA alphabet

DNA sequence

Instances

BioSeq' DNA

Methods

toBS :: DNA a -> ByteString

unsafeFromBS :: ByteString -> DNA a

slice :: Int -> Int -> DNA a -> DNA a

length :: DNA a -> Int

BioSeq DNA Ext

Methods

alphabet :: Proxy * (DNA Ext) -> HashSet Char

fromBS :: ByteString -> Either String (DNA Ext)

BioSeq DNA IUPAC

Methods

alphabet :: Proxy * (DNA IUPAC) -> HashSet Char

fromBS :: ByteString -> Either String (DNA IUPAC)

BioSeq DNA Basic

Methods

alphabet :: Proxy * (DNA Basic) -> HashSet Char

fromBS :: ByteString -> Either String (DNA Basic)

Show (DNA a)

Methods

showsPrec :: Int -> DNA a -> ShowS

show :: DNA a -> String

showList :: [DNA a] -> ShowS

Monoid (DNA a)

Methods

mempty :: DNA a

mappend :: DNA a -> DNA a -> DNA a

mconcat :: [DNA a] -> DNA a

data RNA alphabet

RNA sequence

Instances

BioSeq' RNA

Methods

toBS :: RNA a -> ByteString

unsafeFromBS :: ByteString -> RNA a

slice :: Int -> Int -> RNA a -> RNA a

length :: RNA a -> Int

BioSeq RNA Basic

Methods

alphabet :: Proxy * (RNA Basic) -> HashSet Char

fromBS :: ByteString -> Either String (RNA Basic)

data Peptide alphabet

Peptide sequence

Instances

BioSeq' Peptide

Methods

toBS :: Peptide a -> ByteString

unsafeFromBS :: ByteString -> Peptide a

slice :: Int -> Int -> Peptide a -> Peptide a

length :: Peptide a -> Int

class BioSeq' s where

Minimal complete definition

toBS, slice, unsafeFromBS

Methods

toBS :: s a -> ByteString

unsafeFromBS :: ByteString -> s a

slice :: Int -> Int -> s a -> s a

length :: s a -> Int

Instances

BioSeq' Peptide

Methods

toBS :: Peptide a -> ByteString

unsafeFromBS :: ByteString -> Peptide a

slice :: Int -> Int -> Peptide a -> Peptide a

length :: Peptide a -> Int

BioSeq' RNA

Methods

toBS :: RNA a -> ByteString

unsafeFromBS :: ByteString -> RNA a

slice :: Int -> Int -> RNA a -> RNA a

length :: RNA a -> Int

BioSeq' DNA

Methods

toBS :: DNA a -> ByteString

unsafeFromBS :: ByteString -> DNA a

slice :: Int -> Int -> DNA a -> DNA a

length :: DNA a -> Int

class BioSeq' seq => BioSeq seq alphabet where

Minimal complete definition

alphabet

Methods

alphabet :: Proxy (seq alphabet) -> HashSet Char

fromBS :: ByteString -> Either String (seq alphabet)

Instances

BioSeq RNA Basic

Methods

alphabet :: Proxy * (RNA Basic) -> HashSet Char

fromBS :: ByteString -> Either String (RNA Basic)

BioSeq DNA Ext

Methods

alphabet :: Proxy * (DNA Ext) -> HashSet Char

fromBS :: ByteString -> Either String (DNA Ext)

BioSeq DNA IUPAC

Methods

alphabet :: Proxy * (DNA IUPAC) -> HashSet Char

fromBS :: ByteString -> Either String (DNA IUPAC)

BioSeq DNA Basic

Methods

alphabet :: Proxy * (DNA Basic) -> HashSet Char

fromBS :: ByteString -> Either String (DNA Basic)

DNA related functions

rc :: DNA alphabet -> DNA alphabet

O(n) Reverse complementary of DNA sequence.

gcContent :: DNA alphabet -> Double

O(n) Compute GC content.

nucleotideFreq :: forall a. BioSeq DNA a => DNA a -> HashMap Char Int

O(n) Compute single nucleotide frequency.