Safe Haskell	None
Language	Haskell2010

Biobase.Types.BioSequence

Contents

Sequence identifiers
Bio-Sequences
RNA
DNA
XNA
Amino acid sequences
A window into a longer sequence with prefix/suffix information.
DNA/RNA

Description

Abstraction over bio sequences encoded as one-ascii character as one symbol. We phantom-type the exact bio-sequence type and provide type classes that act on known types.

Unknown bio sequences should be tagged with Void.

TODO give (lens) usage examples

Synopsis

newtype SequenceIdentifier (which :: k) = SequenceIdentifier {
- _sequenceIdentifier :: ByteString
}
_SequenceIdentifier :: forall which which. Iso (SequenceIdentifier which) (SequenceIdentifier which) ByteString ByteString
data RNA
data DNA
data XNA
data AA
newtype BioSequence (which :: k) = BioSequence {
- _bioSequence :: ByteString
}
_BioSequence :: forall which which. Iso (BioSequence which) (BioSequence which) ByteString ByteString
mkRNAseq :: ByteString -> BioSequence RNA
mkDNAseq :: ByteString -> BioSequence DNA
mkXNAseq :: ByteString -> BioSequence XNA
mkAAseq :: ByteString -> BioSequence AA
data BioSequenceWindow w ty loc = BioSequenceWindow {
- _bswIdentifier :: !(SequenceIdentifier w)
- _bswPrefix :: !(BioSequence ty)
- _bswSequence :: !(BioSequence ty)
- _bswSuffix :: !(BioSequence ty)
- _bswLocation :: !loc
}
bswSuffix :: forall w ty loc. Lens' (BioSequenceWindow w ty loc) (BioSequence ty)
bswSequence :: forall w ty loc. Lens' (BioSequenceWindow w ty loc) (BioSequence ty)
bswPrefix :: forall w ty loc. Lens' (BioSequenceWindow w ty loc) (BioSequence ty)
bswLocation :: forall w ty loc loc. Lens (BioSequenceWindow w ty loc) (BioSequenceWindow w ty loc) loc loc
bswIdentifier :: forall w ty loc w. Lens (BioSequenceWindow w ty loc) (BioSequenceWindow w ty loc) (SequenceIdentifier w) (SequenceIdentifier w)
bswFullSequence :: Lens' (BioSequenceWindow w ty k) (BioSequence ty)
attachPrefixes :: Monad m => Stream (Of (BioSequenceWindow w ty k)) m r -> Stream (Of (BioSequenceWindow w ty k)) m r
attachSuffixes :: Monad m => Stream (Of (BioSequenceWindow w ty k)) m r -> Stream (Of (BioSequenceWindow w ty k)) m r
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
reverseComplement :: (Complement f, Reversing f) => Iso' f f

Sequence identifiers

newtype SequenceIdentifier (which :: k) Source #

Constructors

SequenceIdentifier
Fields _sequenceIdentifier :: ByteString

Instances

Eq (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods (==) :: SequenceIdentifier which -> SequenceIdentifier which -> Bool # (/=) :: SequenceIdentifier which -> SequenceIdentifier which -> Bool #
(Typeable which, Typeable k) => Data (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> SequenceIdentifier which -> c (SequenceIdentifier which) # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c (SequenceIdentifier which) # toConstr :: SequenceIdentifier which -> Constr # dataTypeOf :: SequenceIdentifier which -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c (SequenceIdentifier which)) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c (SequenceIdentifier which)) # gmapT :: (forall b. Data b => b -> b) -> SequenceIdentifier which -> SequenceIdentifier which # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> SequenceIdentifier which -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> SequenceIdentifier which -> r # gmapQ :: (forall d. Data d => d -> u) -> SequenceIdentifier which -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> SequenceIdentifier which -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> SequenceIdentifier which -> m (SequenceIdentifier which) # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> SequenceIdentifier which -> m (SequenceIdentifier which) # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> SequenceIdentifier which -> m (SequenceIdentifier which) #
Ord (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods compare :: SequenceIdentifier which -> SequenceIdentifier which -> Ordering # (<) :: SequenceIdentifier which -> SequenceIdentifier which -> Bool # (<=) :: SequenceIdentifier which -> SequenceIdentifier which -> Bool # (>) :: SequenceIdentifier which -> SequenceIdentifier which -> Bool # (>=) :: SequenceIdentifier which -> SequenceIdentifier which -> Bool # max :: SequenceIdentifier which -> SequenceIdentifier which -> SequenceIdentifier which # min :: SequenceIdentifier which -> SequenceIdentifier which -> SequenceIdentifier which #
Read (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods readsPrec :: Int -> ReadS (SequenceIdentifier which) # readList :: ReadS [SequenceIdentifier which] # readPrec :: ReadPrec (SequenceIdentifier which) # readListPrec :: ReadPrec [SequenceIdentifier which] #
Show (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods showsPrec :: Int -> SequenceIdentifier which -> ShowS # show :: SequenceIdentifier which -> String # showList :: [SequenceIdentifier which] -> ShowS #
IsString (SequenceIdentifier w) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> SequenceIdentifier w #
Generic (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence Associated Types type Rep (SequenceIdentifier which) :: Type -> Type # Methods from :: SequenceIdentifier which -> Rep (SequenceIdentifier which) x # to :: Rep (SequenceIdentifier which) x -> SequenceIdentifier which #
NFData (SequenceIdentifier w) Source #
Instance details Defined in Biobase.Types.BioSequence Methods rnf :: SequenceIdentifier w -> () #
Wrapped (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence Associated Types type Unwrapped (SequenceIdentifier which) :: Type # Methods _Wrapped' :: Iso' (SequenceIdentifier which) (Unwrapped (SequenceIdentifier which)) #
SequenceIdentifier which1 ~ t => Rewrapped (SequenceIdentifier which2) t Source #
Instance details Defined in Biobase.Types.BioSequence
type Rep (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence type Rep (SequenceIdentifier which) = D1 (MetaData "SequenceIdentifier" "Biobase.Types.BioSequence" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "SequenceIdentifier" PrefixI True) (S1 (MetaSel (Just "_sequenceIdentifier") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))
type Unwrapped (SequenceIdentifier which) Source #
Instance details Defined in Biobase.Types.BioSequence type Unwrapped (SequenceIdentifier which) = ByteString

_SequenceIdentifier :: forall which which. Iso (SequenceIdentifier which) (SequenceIdentifier which) ByteString ByteString Source #

Bio-Sequences

data RNA Source #

Instances

IsString (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence RNA #
Arbitrary (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods arbitrary :: Gen (BioSequence RNA) # shrink :: BioSequence RNA -> [BioSequence RNA] #
Complement (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods complement :: Iso' (BioSequence RNA) (BioSequence RNA) Source #
Transcribe (BioSequence RNA) Source #	Transcribe a RNA sequence into an DNA sequence. This does not `reverse` the sequence!
Instance details Defined in Biobase.Types.BioSequence Associated Types type TranscribeTo (BioSequence RNA) :: Type Source # Methods transcribe :: Iso' (BioSequence RNA) (TranscribeTo (BioSequence RNA)) Source #
type TranscribeTo (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence type TranscribeTo (BioSequence RNA) = BioSequence DNA

data DNA Source #

Instances

IsString (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence DNA #
Arbitrary (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods arbitrary :: Gen (BioSequence DNA) # shrink :: BioSequence DNA -> [BioSequence DNA] #
Complement (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods complement :: Iso' (BioSequence DNA) (BioSequence DNA) Source #
Transcribe (BioSequence DNA) Source #	Transcribe a DNA sequence into an RNA sequence. This does not `reverse` the sequence!
Instance details Defined in Biobase.Types.BioSequence Associated Types type TranscribeTo (BioSequence DNA) :: Type Source # Methods transcribe :: Iso' (BioSequence DNA) (TranscribeTo (BioSequence DNA)) Source #
type TranscribeTo (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence type TranscribeTo (BioSequence DNA) = BioSequence RNA

data XNA Source #

Instances

IsString (BioSequence XNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence XNA #
Arbitrary (BioSequence XNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods arbitrary :: Gen (BioSequence XNA) # shrink :: BioSequence XNA -> [BioSequence XNA] #

data AA Source #

Instances

IsString (BioSequence AA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence AA #
Arbitrary (BioSequence AA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods arbitrary :: Gen (BioSequence AA) # shrink :: BioSequence AA -> [BioSequence AA] #

newtype BioSequence (which :: k) Source #

Constructors

BioSequence
Fields _bioSequence :: ByteString

Instances

Eq (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods (==) :: BioSequence which -> BioSequence which -> Bool # (/=) :: BioSequence which -> BioSequence which -> Bool #
(Typeable which, Typeable k) => Data (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> BioSequence which -> c (BioSequence which) # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c (BioSequence which) # toConstr :: BioSequence which -> Constr # dataTypeOf :: BioSequence which -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c (BioSequence which)) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c (BioSequence which)) # gmapT :: (forall b. Data b => b -> b) -> BioSequence which -> BioSequence which # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> BioSequence which -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> BioSequence which -> r # gmapQ :: (forall d. Data d => d -> u) -> BioSequence which -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> BioSequence which -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> BioSequence which -> m (BioSequence which) # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> BioSequence which -> m (BioSequence which) # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> BioSequence which -> m (BioSequence which) #
Ord (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods compare :: BioSequence which -> BioSequence which -> Ordering # (<) :: BioSequence which -> BioSequence which -> Bool # (<=) :: BioSequence which -> BioSequence which -> Bool # (>) :: BioSequence which -> BioSequence which -> Bool # (>=) :: BioSequence which -> BioSequence which -> Bool # max :: BioSequence which -> BioSequence which -> BioSequence which # min :: BioSequence which -> BioSequence which -> BioSequence which #
Read (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods readsPrec :: Int -> ReadS (BioSequence which) # readList :: ReadS [BioSequence which] # readPrec :: ReadPrec (BioSequence which) # readListPrec :: ReadPrec [BioSequence which] #
Show (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods showsPrec :: Int -> BioSequence which -> ShowS # show :: BioSequence which -> String # showList :: [BioSequence which] -> ShowS #
IsString (BioSequence Void) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence Void #
IsString (BioSequence AA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence AA #
IsString (BioSequence XNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence XNA #
IsString (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence DNA #
IsString (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods fromString :: String -> BioSequence RNA #
Generic (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence Associated Types type Rep (BioSequence which) :: Type -> Type # Methods from :: BioSequence which -> Rep (BioSequence which) x # to :: Rep (BioSequence which) x -> BioSequence which #
Semigroup (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence Methods (<>) :: BioSequence which -> BioSequence which -> BioSequence which # sconcat :: NonEmpty (BioSequence which) -> BioSequence which # stimes :: Integral b => b -> BioSequence which -> BioSequence which #
Arbitrary (BioSequence AA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods arbitrary :: Gen (BioSequence AA) # shrink :: BioSequence AA -> [BioSequence AA] #
Arbitrary (BioSequence XNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods arbitrary :: Gen (BioSequence XNA) # shrink :: BioSequence XNA -> [BioSequence XNA] #
Arbitrary (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods arbitrary :: Gen (BioSequence DNA) # shrink :: BioSequence DNA -> [BioSequence DNA] #
Arbitrary (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods arbitrary :: Gen (BioSequence RNA) # shrink :: BioSequence RNA -> [BioSequence RNA] #
NFData (BioSequence w) Source #
Instance details Defined in Biobase.Types.BioSequence Methods rnf :: BioSequence w -> () #
Ixed (BioSequence w) Source #
Instance details Defined in Biobase.Types.BioSequence Methods ix :: Index (BioSequence w) -> Traversal' (BioSequence w) (IxValue (BioSequence w)) #
Wrapped (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence Associated Types type Unwrapped (BioSequence which) :: Type # Methods _Wrapped' :: Iso' (BioSequence which) (Unwrapped (BioSequence which)) #
Reversing (BioSequence w) Source #
Instance details Defined in Biobase.Types.BioSequence Methods reversing :: BioSequence w -> BioSequence w #
Complement (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods complement :: Iso' (BioSequence DNA) (BioSequence DNA) Source #
Complement (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods complement :: Iso' (BioSequence RNA) (BioSequence RNA) Source #
Transcribe (BioSequence DNA) Source #	Transcribe a DNA sequence into an RNA sequence. This does not `reverse` the sequence!
Instance details Defined in Biobase.Types.BioSequence Associated Types type TranscribeTo (BioSequence DNA) :: Type Source # Methods transcribe :: Iso' (BioSequence DNA) (TranscribeTo (BioSequence DNA)) Source #
Transcribe (BioSequence RNA) Source #	Transcribe a RNA sequence into an DNA sequence. This does not `reverse` the sequence!
Instance details Defined in Biobase.Types.BioSequence Associated Types type TranscribeTo (BioSequence RNA) :: Type Source # Methods transcribe :: Iso' (BioSequence RNA) (TranscribeTo (BioSequence RNA)) Source #
BioSequence which1 ~ t => Rewrapped (BioSequence which2) t Source #
Instance details Defined in Biobase.Types.BioSequence
type Rep (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence type Rep (BioSequence which) = D1 (MetaData "BioSequence" "Biobase.Types.BioSequence" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" True) (C1 (MetaCons "BioSequence" PrefixI True) (S1 (MetaSel (Just "_bioSequence") NoSourceUnpackedness NoSourceStrictness DecidedLazy) (Rec0 ByteString)))
type Index (BioSequence w) Source #
Instance details Defined in Biobase.Types.BioSequence type Index (BioSequence w) = Int
type IxValue (BioSequence w) Source #
Instance details Defined in Biobase.Types.BioSequence type IxValue (BioSequence w) = Char
type Unwrapped (BioSequence which) Source #
Instance details Defined in Biobase.Types.BioSequence type Unwrapped (BioSequence which) = ByteString
type TranscribeTo (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence type TranscribeTo (BioSequence DNA) = BioSequence RNA
type TranscribeTo (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence type TranscribeTo (BioSequence RNA) = BioSequence DNA

_BioSequence :: forall which which. Iso (BioSequence which) (BioSequence which) ByteString ByteString Source #

RNA

mkRNAseq :: ByteString -> BioSequence RNA Source #

TODO write that converts explicitly

DNA

mkDNAseq :: ByteString -> BioSequence DNA Source #

XNA

mkXNAseq :: ByteString -> BioSequence XNA Source #

Amino acid sequences

mkAAseq :: ByteString -> BioSequence AA Source #

A window into a longer sequence with prefix/suffix information.

data BioSequenceWindow w ty loc Source #

Phantom-typed over two types, the type w of the identifier, which can be descriptive (FirstInput) and the second type, identifying what kind of sequence types we are dealing with. Finally, the third type provides location information and should be location or streamed location.

Constructors

BioSequenceWindow
Fields _bswIdentifier :: !(SequenceIdentifier w) Identifier for this window. Typically some fasta identifier _bswPrefix :: !(BioSequence ty) Any prefix for this sequence _bswSequence :: !(BioSequence ty) The actual sequence, the infix _bswSuffix :: !(BioSequence ty) any suffix _bswLocation :: !loc

Instances

Eq loc => Eq (BioSequenceWindow w ty loc) Source #
Instance details Defined in Biobase.Types.BioSequence Methods (==) :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> Bool # (/=) :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> Bool #
(Typeable w, Typeable ty, Typeable k1, Typeable k2, Data loc) => Data (BioSequenceWindow w ty loc) Source #
Instance details Defined in Biobase.Types.BioSequence Methods gfoldl :: (forall d b. Data d => c (d -> b) -> d -> c b) -> (forall g. g -> c g) -> BioSequenceWindow w ty loc -> c (BioSequenceWindow w ty loc) # gunfold :: (forall b r. Data b => c (b -> r) -> c r) -> (forall r. r -> c r) -> Constr -> c (BioSequenceWindow w ty loc) # toConstr :: BioSequenceWindow w ty loc -> Constr # dataTypeOf :: BioSequenceWindow w ty loc -> DataType # dataCast1 :: Typeable t => (forall d. Data d => c (t d)) -> Maybe (c (BioSequenceWindow w ty loc)) # dataCast2 :: Typeable t => (forall d e. (Data d, Data e) => c (t d e)) -> Maybe (c (BioSequenceWindow w ty loc)) # gmapT :: (forall b. Data b => b -> b) -> BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc # gmapQl :: (r -> r' -> r) -> r -> (forall d. Data d => d -> r') -> BioSequenceWindow w ty loc -> r # gmapQr :: (r' -> r -> r) -> r -> (forall d. Data d => d -> r') -> BioSequenceWindow w ty loc -> r # gmapQ :: (forall d. Data d => d -> u) -> BioSequenceWindow w ty loc -> [u] # gmapQi :: Int -> (forall d. Data d => d -> u) -> BioSequenceWindow w ty loc -> u # gmapM :: Monad m => (forall d. Data d => d -> m d) -> BioSequenceWindow w ty loc -> m (BioSequenceWindow w ty loc) # gmapMp :: MonadPlus m => (forall d. Data d => d -> m d) -> BioSequenceWindow w ty loc -> m (BioSequenceWindow w ty loc) # gmapMo :: MonadPlus m => (forall d. Data d => d -> m d) -> BioSequenceWindow w ty loc -> m (BioSequenceWindow w ty loc) #
Ord loc => Ord (BioSequenceWindow w ty loc) Source #
Instance details Defined in Biobase.Types.BioSequence Methods compare :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> Ordering # (<) :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> Bool # (<=) :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> Bool # (>) :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> Bool # (>=) :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> Bool # max :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc # min :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc #
Read loc => Read (BioSequenceWindow w ty loc) Source #
Instance details Defined in Biobase.Types.BioSequence Methods readsPrec :: Int -> ReadS (BioSequenceWindow w ty loc) # readList :: ReadS [BioSequenceWindow w ty loc] # readPrec :: ReadPrec (BioSequenceWindow w ty loc) # readListPrec :: ReadPrec [BioSequenceWindow w ty loc] #
Show loc => Show (BioSequenceWindow w ty loc) Source #
Instance details Defined in Biobase.Types.BioSequence Methods showsPrec :: Int -> BioSequenceWindow w ty loc -> ShowS # show :: BioSequenceWindow w ty loc -> String # showList :: [BioSequenceWindow w ty loc] -> ShowS #
Generic (BioSequenceWindow w ty loc) Source #
Instance details Defined in Biobase.Types.BioSequence Associated Types type Rep (BioSequenceWindow w ty loc) :: Type -> Type # Methods from :: BioSequenceWindow w ty loc -> Rep (BioSequenceWindow w ty loc) x # to :: Rep (BioSequenceWindow w ty loc) x -> BioSequenceWindow w ty loc #
Reversing loc => Reversing (BioSequenceWindow w ty loc) Source #
Instance details Defined in Biobase.Types.BioSequence Methods reversing :: BioSequenceWindow w ty loc -> BioSequenceWindow w ty loc #
Complement (BioSequence ty) => Complement (BioSequenceWindow w ty k3) Source #
Instance details Defined in Biobase.Types.BioSequence Methods complement :: Iso' (BioSequenceWindow w ty k3) (BioSequenceWindow w ty k3) Source #
type Rep (BioSequenceWindow w ty loc) Source #
Instance details Defined in Biobase.Types.BioSequence type Rep (BioSequenceWindow w ty loc) = D1 (MetaData "BioSequenceWindow" "Biobase.Types.BioSequence" "BiobaseTypes-0.2.0.1-B9coIbijR6NEFcCxvqIOZp" False) (C1 (MetaCons "BioSequenceWindow" PrefixI True) ((S1 (MetaSel (Just "_bswIdentifier") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (SequenceIdentifier w)) :: S1 (MetaSel (Just "_bswPrefix") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (BioSequence ty))) :: (S1 (MetaSel (Just "_bswSequence") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (BioSequence ty)) :: (S1 (MetaSel (Just "_bswSuffix") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 (BioSequence ty)) :: S1 (MetaSel (Just "_bswLocation") NoSourceUnpackedness SourceStrict DecidedStrict) (Rec0 loc)))))

bswSuffix :: forall w ty loc. Lens' (BioSequenceWindow w ty loc) (BioSequence ty) Source #

bswSequence :: forall w ty loc. Lens' (BioSequenceWindow w ty loc) (BioSequence ty) Source #

bswPrefix :: forall w ty loc. Lens' (BioSequenceWindow w ty loc) (BioSequence ty) Source #

bswLocation :: forall w ty loc loc. Lens (BioSequenceWindow w ty loc) (BioSequenceWindow w ty loc) loc loc Source #

bswIdentifier :: forall w ty loc w. Lens (BioSequenceWindow w ty loc) (BioSequenceWindow w ty loc) (SequenceIdentifier w) (SequenceIdentifier w) Source #

bswFullSequence :: Lens' (BioSequenceWindow w ty k) (BioSequence ty) Source #

A lens into the full sequence information of a sequence window. One should *NOT* modify the length of the individual sequences.

attachPrefixes :: Monad m => Stream (Of (BioSequenceWindow w ty k)) m r -> Stream (Of (BioSequenceWindow w ty k)) m r Source #

For each element, attach the prefix as well.

1 2 3 4 -> 01 12 23 34

attachSuffixes :: Monad m => Stream (Of (BioSequenceWindow w ty k)) m r -> Stream (Of (BioSequenceWindow w ty k)) m r Source #

For each element, attach the suffix as well.

1 2 3 4 -> 12 23 34 40

DNA/RNA

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

class Complement f where Source #

The complement of a biosequence.

Methods

complement :: Iso' f f Source #

Instances

Complement (BioSequence DNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods complement :: Iso' (BioSequence DNA) (BioSequence DNA) Source #
Complement (BioSequence RNA) Source #
Instance details Defined in Biobase.Types.BioSequence Methods complement :: Iso' (BioSequence RNA) (BioSequence RNA) Source #
Complement (BioSequence ty) => Complement (BioSequenceWindow w ty k3) Source #
Instance details Defined in Biobase.Types.BioSequence Methods complement :: Iso' (BioSequenceWindow w ty k3) (BioSequenceWindow w ty k3) Source #

reverseComplement :: (Complement f, Reversing f) => Iso' f f Source #