-- | New version, using BlastX results to determine ORFs 

module Main where

import System.IO

import Blastx
import Options

import Bio.Core
import Bio.Core.Sequence.Util 

import Bio.Sequence.Fasta
import BlastFlat

import Control.Monad (when)
import Data.Monoid
import Data.Maybe

main :: IO ()
main = do
  opts <- getOptions
  ss <- readFasta $ fasta opts 
  if gen_all opts 
     then do 
       case cds_out opts of
         "" -> error "No output specified"
         "-" -> hWriteFasta stdout $ concatMap all_frames ss
         cf -> writeFasta cf $ concatMap all_frames ss
     else do
       bs <- readXML $ blastx opts
       h <- case redir_out opts of 
           "" -> return Nothing
           "-" -> return (Just stdout)
           rf -> openFile rf WriteMode >>= \x -> return (Just x)
       g <- case cds_out opts of 
           "" -> return Nothing
           "-" -> return (Just stdout)
           cf -> openFile cf WriteMode >>= \x -> return (Just x)

       let my_process s = do
             when (isJust h) $ process genFasta (fromJust h) s
             when (isJust g) $ process genCDS (fromJust g) s

       mapM_ my_process (frames ss bs)
       when (isJust g) $ hClose (fromJust g)
       when (isJust h) $ hClose (fromJust h)

all_frames :: Sequence -> [Sequence]
all_frames s = 
    map (\i -> (Seq (seqid s <> fromString ("_F+" ++ show i)) (toIUPAC $ translate (seqdata s) i) Nothing)) [0,1,2]
    ++ map (\i -> (Seq (seqid s <> fromString ("_F-" ++ show i)) (toIUPAC $ translate (revcompl $ seqdata s) i) Nothing)) [0,1,2]

process :: (a -> [Sequence]) -> Handle -> a -> IO ()
process fmt h = hWriteFasta h . fmt