Safe Haskell | Safe-Infered |
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- type FastaFunction z = FastaHeader -> StartPos -> WindowSize -> PeekSize -> FastaData -> z
- type StartPos = Int
- type FastaHeader = ByteString
- type FastaData = ByteString
- type WindowSize = Int
- type PeekSize = Int
- rollingIter :: (Monad m, Functor m, Nullable z, Monoid z) => (StartPos -> WindowSize -> PeekSize -> FastaData -> z) -> WindowSize -> PeekSize -> Enumeratee ByteString z m a
- eneeFasta :: (Monad m, Functor m, Nullable z, NullPoint z, Monoid z) => FastaFunction z -> WindowSize -> PeekSize -> Enumeratee ByteString z m a
- fromFile :: (Monoid z, Nullable z) => FastaFunction z -> Int -> Int -> FilePath -> IO z
- fromFileZip :: (Monoid z, Nullable z) => FastaFunction z -> Int -> Int -> FilePath -> IO z

# Documentation

type FastaFunction zSource

= FastaHeader | the > header |

-> StartPos | where in the original sequence to start |

-> WindowSize | how many characters we are looking at |

-> PeekSize | this many characters are from the next window (peeking into) |

-> FastaData | the actual sequence data |

-> z | and what we return as result |

This is the type of the conversion function from FASTA data to the data
`z`

. Make certain that all input is used strictly! BangPatterns are the
easiest to do. In order, the function expects the current FASTA header, then
a data segment, and finally the starting position of the data segment within
the full FASTA data.

If you need the conversion to run in constant time, do not use the convenience functions and replace the final conversion to a strict stream by your own conversion (or output) function.

type FastaHeader = ByteStringSource

Current header (the line starting with `>`

)

type FastaData = ByteStringSource

FASTA data

type WindowSize = IntSource

Window

# conversion from FASTA to data of type `z`

.

rollingIter :: (Monad m, Functor m, Nullable z, Monoid z) => (StartPos -> WindowSize -> PeekSize -> FastaData -> z) -> WindowSize -> PeekSize -> Enumeratee ByteString z m aSource

Takes a bytestring sequence, applies `f`

to each bytestring of windowsize
and returns the results z.

eneeFasta :: (Monad m, Functor m, Nullable z, NullPoint z, Monoid z) => FastaFunction z -> WindowSize -> PeekSize -> Enumeratee ByteString z m aSource

Outer enumeratee. See the two convenience functions for how to use it (just like any enumeratee, basically).

The fasta function `f`

manipulates small stretches of fasta data and has
arguments: fasta header, fasta data, start position (all filled by
eneeFasta).

Next we have the window size, how many characters to read at once,

followed by the the number of characters to read in addition.

The work is actually done by `rollingIter`

.

# Convenience functions: final data is returned strictly.

fromFile :: (Monoid z, Nullable z) => FastaFunction z -> Int -> Int -> FilePath -> IO zSource

From an uncompressed file.

fromFileZip :: (Monoid z, Nullable z) => FastaFunction z -> Int -> Int -> FilePath -> IO zSource

From a gzip-compressed file.