Biobase.Fasta.Streaming

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.

Documentation

data FindHeader

Control structure for streamingFasta.

Constructors

FindHeader

Fields

• headerParts :: [ByteString]

  the collected header parts (in reverse order)

• headerLength :: !Int

  accumulated header length

HasHeader

Fields

• header :: !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

data Current (which :: k)

Current Fasta window, together with the start index (0-based).

Constructors

Current

Fields

• currentFasta :: ByteString
• currentStart :: Index 0

Instances

Eq (Current which)

Defined in Biobase.Fasta.Streaming

Methods

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

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

Ord (Current which)

Defined in Biobase.Fasta.Streaming

Methods

compare :: Current which -> Current which -> Ordering

(<) :: Current which -> Current which -> Bool

(<=) :: Current which -> Current which -> Bool

(>) :: Current which -> Current which -> Bool

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

max :: Current which -> Current which -> Current which

min :: Current which -> Current which -> Current which

Show (Current which)

Defined in Biobase.Fasta.Streaming

Methods

showsPrec :: Int -> Current which -> ShowS

show :: Current which -> String

showList :: [Current which] -> ShowS

newtype Overlap (which :: k)

Constructors

Overlap

Fields

• getOverlap :: ByteString

Instances

Eq (Overlap which)

Defined in Biobase.Fasta.Streaming

Methods

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

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

Ord (Overlap which)

Defined in Biobase.Fasta.Streaming

Methods

compare :: Overlap which -> Overlap which -> Ordering

(<) :: Overlap which -> Overlap which -> Bool

(<=) :: Overlap which -> Overlap which -> Bool

(>) :: Overlap which -> Overlap which -> Bool

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

max :: Overlap which -> Overlap which -> Overlap which

min :: Overlap which -> Overlap which -> Overlap which

Show (Overlap which)

Defined in Biobase.Fasta.Streaming

Methods

showsPrec :: Int -> Overlap which -> ShowS

show :: Overlap which -> String

showList :: [Overlap which] -> ShowS

newtype Header (which :: k)

Constructors

Header

Fields

• getHeader :: ByteString

Instances

Eq (Header which)

Defined in Biobase.Fasta.Streaming

Methods

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

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

Ord (Header which)

Defined in Biobase.Fasta.Streaming

Methods

compare :: Header which -> Header which -> Ordering

(<) :: Header which -> Header which -> Bool

(<=) :: Header which -> Header which -> Bool

(>) :: Header which -> Header which -> Bool

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

max :: Header which -> Header which -> Header which

min :: Header which -> Header which -> Header which

Show (Header which)

Defined in Biobase.Fasta.Streaming

Methods

showsPrec :: Int -> Header which -> ShowS

show :: Header which -> String

showList :: [Header which] -> ShowS

newtype CurrentSize

Constructors

CurrentSize Int

Instances

Eq CurrentSize

Defined in Biobase.Fasta.Streaming

Methods

(==) :: CurrentSize -> CurrentSize -> Bool

(/=) :: CurrentSize -> CurrentSize -> Bool

Ord CurrentSize

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

Defined in Biobase.Fasta.Streaming

Methods

showsPrec :: Int -> CurrentSize -> ShowS

show :: CurrentSize -> String

showList :: [CurrentSize] -> ShowS

newtype OverlapSize

Constructors

OverlapSize Int

Instances

Eq OverlapSize

Defined in Biobase.Fasta.Streaming

Methods

(==) :: OverlapSize -> OverlapSize -> Bool

(/=) :: OverlapSize -> OverlapSize -> Bool

Ord OverlapSize

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

Defined in Biobase.Fasta.Streaming

Methods

showsPrec :: Int -> OverlapSize -> ShowS

show :: OverlapSize -> String

showList :: [OverlapSize] -> ShowS

newtype HeaderSize

Constructors

HeaderSize Int

Instances

Eq HeaderSize

Defined in Biobase.Fasta.Streaming

Methods

(==) :: HeaderSize -> HeaderSize -> Bool

(/=) :: HeaderSize -> HeaderSize -> Bool

Ord HeaderSize

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

Defined in Biobase.Fasta.Streaming

Methods

showsPrec :: Int -> HeaderSize -> ShowS

show :: HeaderSize -> String

showList :: [HeaderSize] -> ShowS

streamingFasta

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.

-> (Header w -> Overlap w -> Current w -> Stream (Of a) m ())

The processing function. Takes in the header, any overlap from the previous window, the current window and produces a stream of as.

-> ByteString m r

A streaming bytestring of Fasta files.

-> Stream (Of a) m r

The outgoing stream of as 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)

eachFasta :: Monad m => Header which1 -> Overlap which2 -> Current which3 -> Stream (Of (ByteString, ByteString, ByteString)) m ()

parseFastaFile :: FilePath -> IO [Fasta]

parseFasta :: ByteString -> [Fasta]