korfu-0.2: src/Korfu.hs

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

module Main where

import System.IO

import Blastx
import Options

import Bio.Sequence
import Bio.Alignment.BlastFlat

import Control.Monad (when)
import Data.Maybe

main :: IO ()
main = do
  opts <- getOptions
  ss <- map castToNuc `fmap` (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 Nuc -> [Sequence Amino]
all_frames s = 
    map (\i -> (Seq (fromStr (toStr (seqlabel s)++"_F+"++show i))  (toIUPAC $ translate s i) Nothing)) [0,1,2]
    ++ map (\i -> (Seq (fromStr (toStr (seqlabel s)++"_F-"++show i)) (toIUPAC $ translate (revcompl s) i) Nothing)) [0,1,2]

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