Biobase.Types.BioSequence

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

Lens operations on biosequences

Sequence identifiers

newtype SequenceIdentifier (which :: k)

Constructors

SequenceIdentifier

Fields

• _sequenceIdentifier :: ByteString

Instances

Eq (SequenceIdentifier which)

Defined in Biobase.Types.BioSequence

Methods

(==) :: SequenceIdentifier which -> SequenceIdentifier which -> Bool

(/=) :: SequenceIdentifier which -> SequenceIdentifier which -> Bool

(Typeable which, Typeable k) => Data (SequenceIdentifier which)

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 :: forall r r'. (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)

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)

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)

Defined in Biobase.Types.BioSequence

Methods

showsPrec :: Int -> SequenceIdentifier which -> ShowS

show :: SequenceIdentifier which -> String

showList :: [SequenceIdentifier which] -> ShowS

IsString (SequenceIdentifier w)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> SequenceIdentifier w

Generic (SequenceIdentifier which)

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)

Defined in Biobase.Types.BioSequence

Methods

rnf :: SequenceIdentifier w -> ()

Wrapped (SequenceIdentifier which)

Defined in Biobase.Types.BioSequence

Associated Types

type Unwrapped (SequenceIdentifier which)

Methods

_Wrapped' :: Iso' (SequenceIdentifier which) (Unwrapped (SequenceIdentifier which))

SequenceIdentifier which1 ~ t => Rewrapped (SequenceIdentifier which2) t

Defined in Biobase.Types.BioSequence

type Rep (SequenceIdentifier which)

Defined in Biobase.Types.BioSequence

type Rep (SequenceIdentifier which) = D1 ('MetaData "SequenceIdentifier" "Biobase.Types.BioSequence" "BiobaseTypes-0.2.1.0-KNWEaQoA0aY419BnftjfF1" 'True) (C1 ('MetaCons "SequenceIdentifier" 'PrefixI 'True) (S1 ('MetaSel ('Just "_sequenceIdentifier") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

type Unwrapped (SequenceIdentifier which)

Defined in Biobase.Types.BioSequence

type Unwrapped (SequenceIdentifier which) = ByteString

_SequenceIdentifier :: forall k (which :: k) k (which :: k). Iso (SequenceIdentifier (which :: k)) (SequenceIdentifier (which :: k)) ByteString ByteString

Bio-Sequences

data RNA

Instances

IsString (BioSequence RNA)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence RNA

Arbitrary (BioSequence RNA)

Defined in Biobase.Types.BioSequence

Methods

arbitrary :: Gen (BioSequence RNA)

shrink :: BioSequence RNA -> [BioSequence RNA]

Complement (BioSequence RNA)

Defined in Biobase.Types.BioSequence

Methods

complement :: Iso' (BioSequence RNA) (BioSequence RNA)

Transcribe (BioSequence RNA)

Transcribe a RNA sequence into an DNA sequence. This does not reverse the sequence!

Defined in Biobase.Types.BioSequence

Associated Types

type TranscribeTo (BioSequence RNA)

Methods

transcribe :: Iso' (BioSequence RNA) (TranscribeTo (BioSequence RNA))

type TranscribeTo (BioSequence RNA)

Defined in Biobase.Types.BioSequence

type TranscribeTo (BioSequence RNA) = BioSequence DNA

data DNA

Instances

IsString (BioSequence DNA)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence DNA

Arbitrary (BioSequence DNA)

Defined in Biobase.Types.BioSequence

Methods

arbitrary :: Gen (BioSequence DNA)

shrink :: BioSequence DNA -> [BioSequence DNA]

Complement (BioSequence DNA)

Defined in Biobase.Types.BioSequence

Methods

complement :: Iso' (BioSequence DNA) (BioSequence DNA)

Transcribe (BioSequence DNA)

Transcribe a DNA sequence into an RNA sequence. This does not reverse the sequence!

Defined in Biobase.Types.BioSequence

Associated Types

type TranscribeTo (BioSequence DNA)

Methods

transcribe :: Iso' (BioSequence DNA) (TranscribeTo (BioSequence DNA))

type TranscribeTo (BioSequence DNA)

Defined in Biobase.Types.BioSequence

type TranscribeTo (BioSequence DNA) = BioSequence RNA

data XNA

Instances

IsString (BioSequence XNA)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence XNA

Arbitrary (BioSequence XNA)

Defined in Biobase.Types.BioSequence

Methods

arbitrary :: Gen (BioSequence XNA)

shrink :: BioSequence XNA -> [BioSequence XNA]

data AA

Instances

IsString (BioSequence AA)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence AA

Arbitrary (BioSequence AA)

Defined in Biobase.Types.BioSequence

Methods

arbitrary :: Gen (BioSequence AA)

shrink :: BioSequence AA -> [BioSequence AA]

newtype BioSequence (which :: k)

TODO provide extended annotation information on biosequences, too!

Constructors

BioSequence

Fields

• _bioSequence :: ByteString

Instances

ModifyLocation FwdPosition (BioSequence w)

Defined in Biobase.Types.Location

Methods

locAppendLeft :: forall k (i :: k). BioSequence w -> Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

locAppendRight :: forall k (i :: k). BioSequence w -> Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

locSplitAt :: forall k (i :: k). Int -> Location i FwdPosition (BioSequence w) -> (Location i FwdPosition (BioSequence w), Location i FwdPosition (BioSequence w))

locLength :: forall k (i :: k). Location i FwdPosition (BioSequence w) -> Int

Eq (BioSequence which)

Defined in Biobase.Types.BioSequence

Methods

(==) :: BioSequence which -> BioSequence which -> Bool

(/=) :: BioSequence which -> BioSequence which -> Bool

(Typeable which, Typeable k) => Data (BioSequence which)

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 :: forall r r'. (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)

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)

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)

Defined in Biobase.Types.BioSequence

Methods

showsPrec :: Int -> BioSequence which -> ShowS

show :: BioSequence which -> String

showList :: [BioSequence which] -> ShowS

IsString (BioSequence Void)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence Void

IsString (BioSequence AA)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence AA

IsString (BioSequence XNA)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence XNA

IsString (BioSequence DNA)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence DNA

IsString (BioSequence RNA)

Defined in Biobase.Types.BioSequence

Methods

fromString :: String -> BioSequence RNA

Generic (BioSequence which)

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)

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

Info (BioSequence w)

Defined in Biobase.Types.BioSequence

Methods

info :: BioSequence w -> String

Arbitrary (BioSequence AA)

Defined in Biobase.Types.BioSequence

Methods

arbitrary :: Gen (BioSequence AA)

shrink :: BioSequence AA -> [BioSequence AA]

Arbitrary (BioSequence XNA)

Defined in Biobase.Types.BioSequence

Methods

arbitrary :: Gen (BioSequence XNA)

shrink :: BioSequence XNA -> [BioSequence XNA]

Arbitrary (BioSequence DNA)

Defined in Biobase.Types.BioSequence

Methods

arbitrary :: Gen (BioSequence DNA)

shrink :: BioSequence DNA -> [BioSequence DNA]

Arbitrary (BioSequence RNA)

Defined in Biobase.Types.BioSequence

Methods

arbitrary :: Gen (BioSequence RNA)

shrink :: BioSequence RNA -> [BioSequence RNA]

Hashable (BioSequence which)

Defined in Biobase.Types.BioSequence

Methods

hashWithSalt :: Int -> BioSequence which -> Int

hash :: BioSequence which -> Int

NFData (BioSequence w)

Defined in Biobase.Types.BioSequence

Methods

rnf :: BioSequence w -> ()

Ixed (BioSequence w)

Defined in Biobase.Types.BioSequence

Methods

ix :: Index (BioSequence w) -> Traversal' (BioSequence w) (IxValue (BioSequence w))

Wrapped (BioSequence which)

Defined in Biobase.Types.BioSequence

Associated Types

type Unwrapped (BioSequence which)

Methods

_Wrapped' :: Iso' (BioSequence which) (Unwrapped (BioSequence which))

Reversing (BioSequence w)

Defined in Biobase.Types.BioSequence

Methods

reversing :: BioSequence w -> BioSequence w

Complement (BioSequence DNA)

Defined in Biobase.Types.BioSequence

Methods

complement :: Iso' (BioSequence DNA) (BioSequence DNA)

Complement (BioSequence RNA)

Defined in Biobase.Types.BioSequence

Methods

complement :: Iso' (BioSequence RNA) (BioSequence RNA)

Transcribe (BioSequence DNA)

Transcribe a DNA sequence into an RNA sequence. This does not reverse the sequence!

Defined in Biobase.Types.BioSequence

Associated Types

type TranscribeTo (BioSequence DNA)

Methods

transcribe :: Iso' (BioSequence DNA) (TranscribeTo (BioSequence DNA))

Transcribe (BioSequence RNA)

Transcribe a RNA sequence into an DNA sequence. This does not reverse the sequence!

Defined in Biobase.Types.BioSequence

Associated Types

type TranscribeTo (BioSequence RNA)

Methods

transcribe :: Iso' (BioSequence RNA) (TranscribeTo (BioSequence RNA))

BioSequence which1 ~ t => Rewrapped (BioSequence which2) t

Defined in Biobase.Types.BioSequence

Info (BioSequence w) => Info (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

info :: Location i FwdPosition (BioSequence w) -> String

Reversing (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

reversing :: Location i FwdPosition (BioSequence w) -> Location i FwdPosition (BioSequence w)

Reversing (Location i FwdPosition (BioSequence w)) => Reversing (PIS i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

reversing :: PIS i FwdPosition (BioSequence w) -> PIS i FwdPosition (BioSequence w)

Complement (BioSequence w) => Complement (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

complement :: Iso' (Location i FwdPosition (BioSequence w)) (Location i FwdPosition (BioSequence w))

Complement (BioSequence w) => Complement (PIS i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

complement :: Iso' (PIS i FwdPosition (BioSequence w)) (PIS i FwdPosition (BioSequence w))

type Rep (BioSequence which)

Defined in Biobase.Types.BioSequence

type Rep (BioSequence which) = D1 ('MetaData "BioSequence" "Biobase.Types.BioSequence" "BiobaseTypes-0.2.1.0-KNWEaQoA0aY419BnftjfF1" 'True) (C1 ('MetaCons "BioSequence" 'PrefixI 'True) (S1 ('MetaSel ('Just "_bioSequence") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

type Index (BioSequence w)

Defined in Biobase.Types.BioSequence

type Index (BioSequence w) = Int

type IxValue (BioSequence w)

Defined in Biobase.Types.BioSequence

type IxValue (BioSequence w) = Char

type Unwrapped (BioSequence which)

Defined in Biobase.Types.BioSequence

type Unwrapped (BioSequence which) = ByteString

type TranscribeTo (BioSequence DNA)

Defined in Biobase.Types.BioSequence

type TranscribeTo (BioSequence DNA) = BioSequence RNA

type TranscribeTo (BioSequence RNA)

Defined in Biobase.Types.BioSequence

type TranscribeTo (BioSequence RNA) = BioSequence DNA

_BioSequence :: forall k (which :: k) k (which :: k). Iso (BioSequence (which :: k)) (BioSequence (which :: k)) ByteString ByteString

bioSequence :: forall k (which :: k) k (which :: k). Iso (BioSequence (which :: k)) (BioSequence (which :: k)) ByteString ByteString

RNA

mkRNAseq :: ByteString -> BioSequence RNA

TODO write that converts explicitly

shrinkBioSequence :: forall k1 k2 (which1 :: k1) (which2 :: k2). BioSequence which1 -> [BioSequence which2]

DNA

mkDNAseq :: ByteString -> BioSequence DNA

XNA

mkXNAseq :: ByteString -> BioSequence XNA

Amino acid sequences

mkAAseq :: ByteString -> BioSequence AA

DNA/RNA

rna2dna :: Char -> Char

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

rnaComplement :: Char -> Char

Single character RNA complement.

dna2rna :: Char -> Char

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

dnaComplement :: Char -> Char

Single character DNA complement.

class Transcribe f where

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 :: *

Methods

transcribe :: Iso' f (TranscribeTo f)

Instances

Transcribe (BioSequence DNA)

Transcribe a DNA sequence into an RNA sequence. This does not reverse the sequence!

Defined in Biobase.Types.BioSequence

Associated Types

type TranscribeTo (BioSequence DNA)

Methods

transcribe :: Iso' (BioSequence DNA) (TranscribeTo (BioSequence DNA))

Transcribe (BioSequence RNA)

Transcribe a RNA sequence into an DNA sequence. This does not reverse the sequence!

Defined in Biobase.Types.BioSequence

Associated Types

type TranscribeTo (BioSequence RNA)

Methods

transcribe :: Iso' (BioSequence RNA) (TranscribeTo (BioSequence RNA))

class Complement f where

The complement of a biosequence.

Methods

complement :: Iso' f f

Instances

Complement (BioSequence DNA)

Defined in Biobase.Types.BioSequence

Methods

complement :: Iso' (BioSequence DNA) (BioSequence DNA)

Complement (BioSequence RNA)

Defined in Biobase.Types.BioSequence

Methods

complement :: Iso' (BioSequence RNA) (BioSequence RNA)

Complement (BioSequence w) => Complement (Location i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

complement :: Iso' (Location i FwdPosition (BioSequence w)) (Location i FwdPosition (BioSequence w))

Complement (BioSequence w) => Complement (PIS i FwdPosition (BioSequence w))

Defined in Biobase.Types.Location

Methods

complement :: Iso' (PIS i FwdPosition (BioSequence w)) (PIS i FwdPosition (BioSequence w))

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