Biobase.Fasta.Strict

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.

Documentation

data Fasta which ty

A *strict* Fasta entry.

Constructors

Fasta

Fields

• _header :: !(SequenceIdentifier which)
• _fasta :: !(BioSequence ty)

Instances

Eq (Fasta which ty)

Defined in Biobase.Fasta.Strict

Methods

(==) :: Fasta which ty -> Fasta which ty -> Bool

(/=) :: Fasta which ty -> Fasta which ty -> Bool

Ord (Fasta which ty)

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)

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)

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)

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)

Defined in Biobase.Fasta.Strict

type Rep (Fasta which ty) = D1 (MetaData "Fasta" "Biobase.Fasta.Strict" "BiobaseFasta-0.3.0.0-HIBNGtakS1j401lJ1LmiCG" 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

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

fasta :: forall which ty ty. Lens (Fasta which ty) (Fasta which ty) (BioSequence ty) (BioSequence ty)

header :: forall which ty which. Lens (Fasta which ty) (Fasta which ty) (SequenceIdentifier which) (SequenceIdentifier which)

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

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

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

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

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

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

byteStringToMultiFasta :: ByteString -> [Fasta which ty]

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

windowedFasta :: Lens' (BioSequenceWindow w ty k) (Fasta w ty)

A lens that goes from a BioSequenceWindow to a Fasta.

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

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