Safe Haskell	None
Language	Haskell2010

Biobase.Fasta.Streaming

Description

Streaming Fasta handling via the streaming library.

The functions in here should be streaming in constant memory.

TODO Check if this is actually true with some unit tests.

Synopsis

data FindHeader
- = FindHeader {
  - headerParts :: [ByteString]
  - headerLength :: !Int
  }
- | HasHeader {
  - fhHeader :: !ByteString
  - dataOverlap :: !ByteString
  - dataParts :: [ByteString]
  - dataLength :: !Int
  - entries :: !Int
  }
newtype CurrentSize = CurrentSize Int
newtype OverlapSize = OverlapSize Int
newtype HeaderSize = HeaderSize Int
fastaUid :: Lens' (SequenceIdentifier w) ByteString
streamingFasta :: forall m w ty k r a. Monad m => HeaderSize -> OverlapSize -> CurrentSize -> ByteString m r -> Stream (Of (BioSequenceWindow w ty k)) m r

Documentation

data FindHeader Source #

Control structure for streamingFasta.

Constructors

FindHeader
Fields headerParts :: [ByteString] the collected header parts (in reverse order) headerLength :: !Int accumulated header length
HasHeader
Fields fhHeader :: !ByteString the (size-truncated) header for this fasta file dataOverlap :: !ByteString overlap (if any) from earlier parts of the fasta file dataParts :: [ByteString] collection of dataParts, in reverse order! dataLength :: !Int total length of data parts, simplifies checking if enough data was collected entries :: !Int count how many entries we have seen

newtype CurrentSize Source #

Constructors

CurrentSize Int

Instances

Eq CurrentSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods (==) :: CurrentSize -> CurrentSize -> Bool # (/=) :: CurrentSize -> CurrentSize -> Bool #
Ord CurrentSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods compare :: CurrentSize -> CurrentSize -> Ordering # (<) :: CurrentSize -> CurrentSize -> Bool # (<=) :: CurrentSize -> CurrentSize -> Bool # (>) :: CurrentSize -> CurrentSize -> Bool # (>=) :: CurrentSize -> CurrentSize -> Bool # max :: CurrentSize -> CurrentSize -> CurrentSize # min :: CurrentSize -> CurrentSize -> CurrentSize #
Show CurrentSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods showsPrec :: Int -> CurrentSize -> ShowS # show :: CurrentSize -> String # showList :: [CurrentSize] -> ShowS #

newtype OverlapSize Source #

Constructors

OverlapSize Int

Instances

Eq OverlapSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods (==) :: OverlapSize -> OverlapSize -> Bool # (/=) :: OverlapSize -> OverlapSize -> Bool #
Ord OverlapSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods compare :: OverlapSize -> OverlapSize -> Ordering # (<) :: OverlapSize -> OverlapSize -> Bool # (<=) :: OverlapSize -> OverlapSize -> Bool # (>) :: OverlapSize -> OverlapSize -> Bool # (>=) :: OverlapSize -> OverlapSize -> Bool # max :: OverlapSize -> OverlapSize -> OverlapSize # min :: OverlapSize -> OverlapSize -> OverlapSize #
Show OverlapSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods showsPrec :: Int -> OverlapSize -> ShowS # show :: OverlapSize -> String # showList :: [OverlapSize] -> ShowS #

newtype HeaderSize Source #

Constructors

HeaderSize Int

Instances

Eq HeaderSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods (==) :: HeaderSize -> HeaderSize -> Bool # (/=) :: HeaderSize -> HeaderSize -> Bool #
Ord HeaderSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods compare :: HeaderSize -> HeaderSize -> Ordering # (<) :: HeaderSize -> HeaderSize -> Bool # (<=) :: HeaderSize -> HeaderSize -> Bool # (>) :: HeaderSize -> HeaderSize -> Bool # (>=) :: HeaderSize -> HeaderSize -> Bool # max :: HeaderSize -> HeaderSize -> HeaderSize # min :: HeaderSize -> HeaderSize -> HeaderSize #
Show HeaderSize Source #
Instance details Defined in Biobase.Fasta.Streaming Methods showsPrec :: Int -> HeaderSize -> ShowS # show :: HeaderSize -> String # showList :: [HeaderSize] -> ShowS #

fastaUid :: Lens' (SequenceIdentifier w) ByteString Source #

lens into the unique id / first word of the header.

streamingFasta Source #

Arguments

:: Monad m
=> HeaderSize	Maximal length of the header. Ok to set to `20 000`, only guards against an extremely long header line.
-> OverlapSize	How much of the current size to carry over to the next step. Even if set larger than current size, it will only be at most current size. (But see todo at `overlappedFasta`)
-> CurrentSize	The size of each window to be processed.
-> ByteString m r	A streaming bytestring of Fasta files.
-> Stream (Of (BioSequenceWindow w ty k)) m r	The outgoing stream of `Current` windows being processed.

Fully stream a fasta file, making sure to never exceed a constant amount of memory. The go function yields values of type a down the line for continued streaming.

r4 = toList . streamingFasta (HeaderSize 2) (OverlapSize 1) (CurrentSize 2) go . S8.fromStrict $ BS.pack t0
 where go (Header h) (Overlap o) (Current c) = yield (h,o,c)