Safe Haskell	None
Language	Haskell2010

Biobase.Types.NucleotideSequence

Description

Wrappers around biosequences.

Synopsis

newtype SequenceID = SequenceID {
- _sequenceID :: ByteString
}
sequenceID :: Iso' SequenceID ByteString
sequenceIDstring :: Iso' SequenceID String
newtype RNAseq = RNAseq {
- _rnaseq :: ByteString
}
rnaseq :: Iso' RNAseq ByteString
mkRNAseq :: ByteString -> RNAseq
newtype DNAseq = DNAseq {
- _dnaseq :: ByteString
}
dnaseq :: Iso' DNAseq ByteString
mkDNAseq :: ByteString -> DNAseq
rna2dna :: Char -> Char
rnaComplement :: Char -> Char
dna2rna :: Char -> Char
dnaComplement :: Char -> Char
class Transcribe f where
- type TranscribeTo f :: *
- transcribe :: Iso' f (TranscribeTo f)
class Complement f where
- complement :: Iso' f f

Documentation

newtype SequenceID Source #

A sequence identifier. Just a newtype wrapped text field. Because we can never know what people are up to, this is utf8-encoded.

TODO Provide Iso' for Text, too?

TODO move into Biobase.Types.SequenceID

Constructors

SequenceID
Fields _sequenceID :: ByteString

Instances

Eq SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods (==) :: SequenceID -> SequenceID -> Bool # (/=) :: SequenceID -> SequenceID -> Bool #
Data SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> SequenceID -> c SequenceID # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c SequenceID # toConstr :: SequenceID -> Constr # dataTypeOf :: SequenceID -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c SequenceID) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c SequenceID) # gmapT :: (forall b. Data b => b -> b) -> SequenceID -> SequenceID # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> SequenceID -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> SequenceID -> r # gmapQ :: (forall d. Data d => d -> u) -> SequenceID -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> SequenceID -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> SequenceID -> m SequenceID # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> SequenceID -> m SequenceID # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> SequenceID -> m SequenceID #
Ord SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods compare :: SequenceID -> SequenceID -> Ordering # (<) :: SequenceID -> SequenceID -> Bool # (<=) :: SequenceID -> SequenceID -> Bool # (>) :: SequenceID -> SequenceID -> Bool # (>=) :: SequenceID -> SequenceID -> Bool # max :: SequenceID -> SequenceID -> SequenceID # min :: SequenceID -> SequenceID -> SequenceID #
Read SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods readsPrec :: Int -> ReadS SequenceID # readList :: ReadS [SequenceID] # readPrec :: ReadPrec SequenceID # readListPrec :: ReadPrec [SequenceID] #
Show SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods showsPrec :: Int -> SequenceID -> ShowS # show :: SequenceID -> String # showList :: [SequenceID] -> ShowS #
IsString SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods fromString :: String -> SequenceID #
Generic SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence Associated Types type Rep SequenceID :: Type -> Type # Methods from :: SequenceID -> Rep SequenceID x # to :: Rep SequenceID x -> SequenceID #
NFData SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods rnf :: SequenceID -> () #
type Rep SequenceID Source #
Instance details Defined in Biobase.Types.NucleotideSequence type Rep SequenceID = D1 (MetaData "SequenceID" "Biobase.Types.NucleotideSequence" "BiobaseTypes-0.1.4.0-2SJmLmHyrafG90Dl3d2I5j" True) (C1 (MetaCons "SequenceID" PrefixI True) (S1 (MetaSel (Just "_sequenceID") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))

sequenceID :: Iso' SequenceID ByteString Source #

sequenceIDstring :: Iso' SequenceID String Source #

Convert to a string in a unicode-aware manner.

newtype RNAseq Source #

A short RNA sequence.

It is an instance of Ixed to allow RNAseq (BS.pack "cag") ^? ix 2 == Just g.

Constructors

RNAseq
Fields _rnaseq :: ByteString

Instances

Eq RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods (==) :: RNAseq -> RNAseq -> Bool # (/=) :: RNAseq -> RNAseq -> Bool #
Data RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> RNAseq -> c RNAseq # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c RNAseq # toConstr :: RNAseq -> Constr # dataTypeOf :: RNAseq -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c RNAseq) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c RNAseq) # gmapT :: (forall b. Data b => b -> b) -> RNAseq -> RNAseq # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> RNAseq -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> RNAseq -> r # gmapQ :: (forall d. Data d => d -> u) -> RNAseq -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> RNAseq -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> RNAseq -> m RNAseq # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAseq -> m RNAseq # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> RNAseq -> m RNAseq #
Ord RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods compare :: RNAseq -> RNAseq -> Ordering # (<) :: RNAseq -> RNAseq -> Bool # (<=) :: RNAseq -> RNAseq -> Bool # (>) :: RNAseq -> RNAseq -> Bool # (>=) :: RNAseq -> RNAseq -> Bool # max :: RNAseq -> RNAseq -> RNAseq # min :: RNAseq -> RNAseq -> RNAseq #
Read RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods readsPrec :: Int -> ReadS RNAseq # readList :: ReadS [RNAseq] # readPrec :: ReadPrec RNAseq # readListPrec :: ReadPrec [RNAseq] #
Show RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods showsPrec :: Int -> RNAseq -> ShowS # show :: RNAseq -> String # showList :: [RNAseq] -> ShowS #
IsString RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods fromString :: String -> RNAseq #
Generic RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Associated Types type Rep RNAseq :: Type -> Type # Methods from :: RNAseq -> Rep RNAseq x # to :: Rep RNAseq x -> RNAseq #
Arbitrary RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods arbitrary :: Gen RNAseq # shrink :: RNAseq -> [RNAseq] #
NFData RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods rnf :: RNAseq -> () #
Ixed RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods ix :: Index RNAseq -> Traversal' RNAseq (IxValue RNAseq) #
Reversing RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods reversing :: RNAseq -> RNAseq #
Complement RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods complement :: Iso' RNAseq RNAseq Source #
Transcribe RNAseq Source #	Transcribe a RNA sequence into an DNA sequence. This does not `reverse` the sequence!
Instance details Defined in Biobase.Types.NucleotideSequence Associated Types type TranscribeTo RNAseq :: Type Source # Methods transcribe :: Iso' RNAseq (TranscribeTo RNAseq) Source #
type Rep RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence type Rep RNAseq = D1 (MetaData "RNAseq" "Biobase.Types.NucleotideSequence" "BiobaseTypes-0.1.4.0-2SJmLmHyrafG90Dl3d2I5j" True) (C1 (MetaCons "RNAseq" PrefixI True) (S1 (MetaSel (Just "_rnaseq") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))
type Index RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence type Index RNAseq = Int
type IxValue RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence type IxValue RNAseq = Char
type TranscribeTo RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence type TranscribeTo RNAseq = DNAseq

rnaseq :: Iso' RNAseq ByteString Source #

mkRNAseq :: ByteString -> RNAseq Source #

newtype DNAseq Source #

A short DNA sequence.

Note everything really long should be handled by specialized libraries with streaming capabilities.

Constructors

DNAseq
Fields _dnaseq :: ByteString

Instances

Eq DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods (==) :: DNAseq -> DNAseq -> Bool # (/=) :: DNAseq -> DNAseq -> Bool #
Data DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> DNAseq -> c DNAseq # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c DNAseq # toConstr :: DNAseq -> Constr # dataTypeOf :: DNAseq -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c DNAseq) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c DNAseq) # gmapT :: (forall b. Data b => b -> b) -> DNAseq -> DNAseq # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> DNAseq -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> DNAseq -> r # gmapQ :: (forall d. Data d => d -> u) -> DNAseq -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> DNAseq -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> DNAseq -> m DNAseq # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> DNAseq -> m DNAseq # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> DNAseq -> m DNAseq #
Ord DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods compare :: DNAseq -> DNAseq -> Ordering # (<) :: DNAseq -> DNAseq -> Bool # (<=) :: DNAseq -> DNAseq -> Bool # (>) :: DNAseq -> DNAseq -> Bool # (>=) :: DNAseq -> DNAseq -> Bool # max :: DNAseq -> DNAseq -> DNAseq # min :: DNAseq -> DNAseq -> DNAseq #
Read DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods readsPrec :: Int -> ReadS DNAseq # readList :: ReadS [DNAseq] # readPrec :: ReadPrec DNAseq # readListPrec :: ReadPrec [DNAseq] #
Show DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods showsPrec :: Int -> DNAseq -> ShowS # show :: DNAseq -> String # showList :: [DNAseq] -> ShowS #
IsString DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods fromString :: String -> DNAseq #
Generic DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Associated Types type Rep DNAseq :: Type -> Type # Methods from :: DNAseq -> Rep DNAseq x # to :: Rep DNAseq x -> DNAseq #
Arbitrary DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods arbitrary :: Gen DNAseq # shrink :: DNAseq -> [DNAseq] #
NFData DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods rnf :: DNAseq -> () #
Ixed DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods ix :: Index DNAseq -> Traversal' DNAseq (IxValue DNAseq) #
Reversing DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods reversing :: DNAseq -> DNAseq #
Complement DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods complement :: Iso' DNAseq DNAseq Source #
Transcribe DNAseq Source #	Transcribe a DNA sequence into an RNA sequence. This does not `reverse` the sequence!
Instance details Defined in Biobase.Types.NucleotideSequence Associated Types type TranscribeTo DNAseq :: Type Source # Methods transcribe :: Iso' DNAseq (TranscribeTo DNAseq) Source #
type Rep DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence type Rep DNAseq = D1 (MetaData "DNAseq" "Biobase.Types.NucleotideSequence" "BiobaseTypes-0.1.4.0-2SJmLmHyrafG90Dl3d2I5j" True) (C1 (MetaCons "DNAseq" PrefixI True) (S1 (MetaSel (Just "_dnaseq") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))
type Index DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence type Index DNAseq = Int
type IxValue DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence type IxValue DNAseq = Char
type TranscribeTo DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence type TranscribeTo DNAseq = RNAseq

dnaseq :: Iso' DNAseq ByteString Source #

mkDNAseq :: ByteString -> DNAseq Source #

rna2dna :: Char -> Char Source #

Simple case translation from U to T. with upper and lower-case awareness.

rnaComplement :: Char -> Char Source #

Single character RNA complement.

dna2rna :: Char -> Char Source #

Simple case translation from T to U with upper- and lower-case awareness.

dnaComplement :: Char -> Char Source #

Single character DNA complement.

class Transcribe f where Source #

Transcribes a DNA sequence into an RNA sequence. Note that transcribe is actually very generic. We just define its semantics to be that of biomolecular transcription.

transcribe makes the assumption that, given DNA -> RNA, we transcribe the coding strand. http://hyperphysics.phy-astr.gsu.edu/hbase/Organic/transcription.html

@DNAseq ACGT ^. transcribe == RNAseq ACGU RNAseq ACGU ^. transcribe == DNAseq ACGT RNAseq ACGU ^. from transcribe :: DNAseq == DNAseq ACGT@

Associated Types

type TranscribeTo f :: * Source #

Methods

transcribe :: Iso' f (TranscribeTo f) Source #

Instances

Transcribe RNAseq Source #	Transcribe a RNA sequence into an DNA sequence. This does not `reverse` the sequence!
Instance details Defined in Biobase.Types.NucleotideSequence Associated Types type TranscribeTo RNAseq :: Type Source # Methods transcribe :: Iso' RNAseq (TranscribeTo RNAseq) Source #
Transcribe DNAseq Source #	Transcribe a DNA sequence into an RNA sequence. This does not `reverse` the sequence!
Instance details Defined in Biobase.Types.NucleotideSequence Associated Types type TranscribeTo DNAseq :: Type Source # Methods transcribe :: Iso' DNAseq (TranscribeTo DNAseq) Source #

class Complement f where Source #

The complement of a biosequence.

Methods

complement :: Iso' f f Source #

Instances

Complement RNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods complement :: Iso' RNAseq RNAseq Source #
Complement DNAseq Source #
Instance details Defined in Biobase.Types.NucleotideSequence Methods complement :: Iso' DNAseq DNAseq Source #