Re: Binning k-mers, open file handle question

[Youens-Clark, Charles Kenneth - (kyclark)]

On Jul 25, 2015, at 10:43 AM, Nicholas Ingolia <n...@ingolia.org> wrote:
> 
> I would suggest opening all files at the beginning. Generate all k-mers,
> open a file for each, and make a HashMap from k-mer to file handle. When
> you're done, run through the HashMap to close all file handles. 

I really like this idea and feel I'm close to having something that works.  
Here's a bit:

main = do
  reads <- readFasta "test.fa"
  let kmers       = concatMap (findKmers 20 . toString . seqdata) reads
  let allMers     = replicateM 5 "ACTG"
  let fileHandles = Map.fromList $
                    map (\x -> (x, openFile ("out/" ++ x) WriteMode)) allMers

  mapM_ (printMer fileHandles) kmers

  mapM_ hClose $ Map.elems fileHandles

Here "fileHandles" type is:

fileHandles :: Map.Map [Char] (IO Handle)

But it would be much easier if the elems were just Handle's.  Is there a way to 
do this?  I tried this:

  let fileHandles = Map.fromList $
                    map (\x -> do h <- openFile ("out/" ++ x) WriteMode
                                  (x, h))
                    allMers

I'm still really hung up on the whole IO monad thing.

Ken