Safe Haskell	None
Language	Haskell2010

Biobase.Types.Sequence

Description

Wrappers around biosequences.

Synopsis

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?

Constructors

SequenceID
Fields _sequenceID :: ByteString

Instances

Eq SequenceID Source #
Methods (==) :: SequenceID -> SequenceID -> Bool # (/=) :: SequenceID -> SequenceID -> Bool #
Data SequenceID Source #
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 #
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 #
Methods readsPrec :: Int -> ReadS SequenceID # readList :: ReadS [SequenceID] # readPrec :: ReadPrec SequenceID # readListPrec :: ReadPrec [SequenceID] #
Show SequenceID Source #
Methods showsPrec :: Int -> SequenceID -> ShowS # show :: SequenceID -> String # showList :: [SequenceID] -> ShowS #
IsString SequenceID Source #
Methods fromString :: String -> SequenceID #
Generic SequenceID Source #
Associated Types type Rep SequenceID :: * -> * # Methods from :: SequenceID -> Rep SequenceID x # to :: Rep SequenceID x -> SequenceID #
NFData SequenceID Source #
Methods rnf :: SequenceID -> () #
type Rep SequenceID Source #
type Rep SequenceID = D1 (MetaData "SequenceID" "Biobase.Types.Sequence" "BiobaseTypes-0.1.3.0-7EMqsaldKh99G4UiC4Kzi1" True) (C1 (MetaCons "SequenceID" PrefixI True) (S1 (MetaSel (Just Symbol "_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 #
Methods (==) :: RNAseq -> RNAseq -> Bool # (/=) :: RNAseq -> RNAseq -> Bool #
Data RNAseq Source #
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 #
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 #
Methods readsPrec :: Int -> ReadS RNAseq # readList :: ReadS [RNAseq] # readPrec :: ReadPrec RNAseq # readListPrec :: ReadPrec [RNAseq] #
Show RNAseq Source #
Methods showsPrec :: Int -> RNAseq -> ShowS # show :: RNAseq -> String # showList :: [RNAseq] -> ShowS #
IsString RNAseq Source #
Methods fromString :: String -> RNAseq #
Generic RNAseq Source #
Associated Types type Rep RNAseq :: * -> * # Methods from :: RNAseq -> Rep RNAseq x # to :: Rep RNAseq x -> RNAseq #
NFData RNAseq Source #
Methods rnf :: RNAseq -> () #
Ixed RNAseq Source #
Methods ix :: Index RNAseq -> Traversal' RNAseq (IxValue RNAseq) #
Reversing RNAseq Source #
Methods reversing :: RNAseq -> RNAseq #
Complement RNAseq Source #
Methods complement :: Iso' RNAseq RNAseq Source #
Transcribe RNAseq Source #	Transcribe a RNA sequence into an DNA sequence. This does not `reverse` the sequence!
Associated Types type TranscribeTo RNAseq :: * Source # Methods transcribe :: Iso' RNAseq (TranscribeTo RNAseq) Source #
type Rep RNAseq Source #
type Rep RNAseq = D1 (MetaData "RNAseq" "Biobase.Types.Sequence" "BiobaseTypes-0.1.3.0-7EMqsaldKh99G4UiC4Kzi1" True) (C1 (MetaCons "RNAseq" PrefixI True) (S1 (MetaSel (Just Symbol "_rnaseq") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))
type Index RNAseq Source #
type Index RNAseq = Int
type IxValue RNAseq Source #
type IxValue RNAseq = Char
type TranscribeTo RNAseq Source #
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 #
Methods (==) :: DNAseq -> DNAseq -> Bool # (/=) :: DNAseq -> DNAseq -> Bool #
Data DNAseq Source #
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 #
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 #
Methods readsPrec :: Int -> ReadS DNAseq # readList :: ReadS [DNAseq] # readPrec :: ReadPrec DNAseq # readListPrec :: ReadPrec [DNAseq] #
Show DNAseq Source #
Methods showsPrec :: Int -> DNAseq -> ShowS # show :: DNAseq -> String # showList :: [DNAseq] -> ShowS #
IsString DNAseq Source #
Methods fromString :: String -> DNAseq #
Generic DNAseq Source #
Associated Types type Rep DNAseq :: * -> * # Methods from :: DNAseq -> Rep DNAseq x # to :: Rep DNAseq x -> DNAseq #
NFData DNAseq Source #
Methods rnf :: DNAseq -> () #
Ixed DNAseq Source #
Methods ix :: Index DNAseq -> Traversal' DNAseq (IxValue DNAseq) #
Reversing DNAseq Source #
Methods reversing :: DNAseq -> DNAseq #
Complement DNAseq Source #
Methods complement :: Iso' DNAseq DNAseq Source #
Transcribe DNAseq Source #	Transcribe a DNA sequence into an RNA sequence. This does not `reverse` the sequence!
Associated Types type TranscribeTo DNAseq :: * Source # Methods transcribe :: Iso' DNAseq (TranscribeTo DNAseq) Source #
type Rep DNAseq Source #
type Rep DNAseq = D1 (MetaData "DNAseq" "Biobase.Types.Sequence" "BiobaseTypes-0.1.3.0-7EMqsaldKh99G4UiC4Kzi1" True) (C1 (MetaCons "DNAseq" PrefixI True) (S1 (MetaSel (Just Symbol "_dnaseq") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))
type Index DNAseq Source #
type Index DNAseq = Int
type IxValue DNAseq Source #
type IxValue DNAseq = Char
type TranscribeTo DNAseq Source #
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@

Minimal complete definition

transcribe

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!
Associated Types type TranscribeTo RNAseq :: * 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!
Associated Types type TranscribeTo DNAseq :: * Source # Methods transcribe :: Iso' DNAseq (TranscribeTo DNAseq) Source #

class Complement f where Source #

The complement of a biosequence.

Minimal complete definition

complement

Methods

complement :: Iso' f f Source #

Instances

Complement RNAseq Source #
Methods complement :: Iso' RNAseq RNAseq Source #
Complement DNAseq Source #
Methods complement :: Iso' DNAseq DNAseq Source #