Safe Haskell	None
Language	Haskell2010

Biobase.Fasta.Strict

Description

A convenience module for *small* Fasta entries, that are completely in memory and *not* to be streamed.

The Data.ByteString.Strict.Lens module is very helpful for further handling of Fasta entries.

For convenience, the convertString function from string-conversions is supplied.

Synopsis

data Fasta which ty = Fasta {
- _header :: !(SequenceIdentifier which)
- _fasta :: !(BioSequence ty)
}
type FastaUntyped = Fasta Void Void
fasta :: forall k (which :: k) k (ty :: k) k (ty :: k). Lens (Fasta (which :: k) (ty :: k)) (Fasta (which :: k) (ty :: k)) (BioSequence ty) (BioSequence ty)
header :: forall k (which :: k) k (ty :: k) k (which :: k). Lens (Fasta (which :: k) (ty :: k)) (Fasta (which :: k) (ty :: k)) (SequenceIdentifier which) (SequenceIdentifier which)
fastaToByteString :: Int -> Fasta which ty -> ByteString
fastaToBuilder :: Int -> Fasta which ty -> Builder
byteStringToFasta :: ByteString -> Either String (Fasta which ty)
rawFasta :: Int -> Prism' ByteString (Fasta which ty)
convertString :: ConvertibleStrings a b => a -> b

Documentation

data Fasta which ty Source #

A *strict* Fasta entry.

Constructors

Fasta
Fields _header :: !(SequenceIdentifier which) _fasta :: !(BioSequence ty)

Instances

Instances details

Eq (Fasta which ty) Source #
Instance details Defined in Biobase.Fasta.Strict Methods (==) :: Fasta which ty -> Fasta which ty -> Bool # (/=) :: Fasta which ty -> Fasta which ty -> Bool #
Ord (Fasta which ty) Source #
Instance details Defined in Biobase.Fasta.Strict Methods compare :: Fasta which ty -> Fasta which ty -> Ordering # (<) :: Fasta which ty -> Fasta which ty -> Bool # (<=) :: Fasta which ty -> Fasta which ty -> Bool # (>) :: Fasta which ty -> Fasta which ty -> Bool # (>=) :: Fasta which ty -> Fasta which ty -> Bool # max :: Fasta which ty -> Fasta which ty -> Fasta which ty # min :: Fasta which ty -> Fasta which ty -> Fasta which ty #
Read (Fasta which ty) Source #
Instance details Defined in Biobase.Fasta.Strict Methods readsPrec :: Int -> ReadS (Fasta which ty) # readList :: ReadS [Fasta which ty] # readPrec :: ReadPrec (Fasta which ty) # readListPrec :: ReadPrec [Fasta which ty] #
Show (Fasta which ty) Source #
Instance details Defined in Biobase.Fasta.Strict Methods showsPrec :: Int -> Fasta which ty -> ShowS # show :: Fasta which ty -> String # showList :: [Fasta which ty] -> ShowS #
Generic (Fasta which ty) Source #
Instance details Defined in Biobase.Fasta.Strict Associated Types type Rep (Fasta which ty) :: Type -> Type # Methods from :: Fasta which ty -> Rep (Fasta which ty) x # to :: Rep (Fasta which ty) x -> Fasta which ty #
type Rep (Fasta which ty) Source #
Instance details Defined in Biobase.Fasta.Strict type Rep (Fasta which ty) = D1 ('MetaData "Fasta" "Biobase.Fasta.Strict" "BiobaseFasta-0.4.0.1-I5UInIvAd7s5DuuDcsslQC" 'False) (C1 ('MetaCons "Fasta" 'PrefixI 'True) (S1 ('MetaSel ('Just "_header") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (SequenceIdentifier which)) :*: S1 ('MetaSel ('Just "_fasta") 'NoSourceUnpackedness 'SourceStrict 'DecidedStrict) (Rec0 (BioSequence ty))))

type FastaUntyped = Fasta Void Void Source #

If you don't want to deal with the phantom types.

fasta :: forall k (which :: k) k (ty :: k) k (ty :: k). Lens (Fasta (which :: k) (ty :: k)) (Fasta (which :: k) (ty :: k)) (BioSequence ty) (BioSequence ty) Source #

header :: forall k (which :: k) k (ty :: k) k (which :: k). Lens (Fasta (which :: k) (ty :: k)) (Fasta (which :: k) (ty :: k)) (SequenceIdentifier which) (SequenceIdentifier which) Source #

fastaToByteString :: Int -> Fasta which ty -> ByteString Source #

Render a Fasta entry to a ByteString. Will end with a final n in any case.

fastaToBuilder :: Int -> Fasta which ty -> Builder Source #

Render a Fasta entry to a Builder. Will end with a final n in any case.

byteStringToFasta :: ByteString -> Either String (Fasta which ty) Source #

Try to parse a ByteString as a Fasta, failing with Left, succees with Right.

rawFasta :: Int -> Prism' ByteString (Fasta which ty) Source #

Try to parse a ByteString as multiple Fasta entries. Even though this is using the underlying streaming interface, this is not streaming.

A lens that goes from a BioSequenceWindow to a Fasta.

A prism from a ByteString to a Fasta. Note that this will only be an identity if the underlying fasta file is rendered with k characters per line.

convertString :: ConvertibleStrings a b => a -> b #