korfu-0.2: src/Options.hs

module Options where

import System.Environment (getArgs)
import System.Console.GetOpt
import System (exitWith,ExitCode(..))
import Control.Monad

-- import Bio.Util (countIO)

getOptions :: IO Options
getOptions  = do as <- getArgs
                 let (optf,non,err) = getOpt Permute options as
                 when (not (null err && null non)) $ error (usage err)
                 if null as
                     then normalUsage
                     else parseargs optf

normalUsage :: IO a
normalUsage = do
  putStrLn $ usageInfo (usagemsg++synopsis) options
  exitWith ExitSuccess

usage :: [String] -> String
usage errs = usageInfo (concat errs ++ usagemsg) options

usagemsg, synopsis :: String
usagemsg = "Usage: korfu -i <file> -x <file.xml> [-R <file>] [-C <file>]\n"
synopsis = "Characterize ESTs using BLASTX hits and sequence heuristics.\n"

data Options = Opts { redir_out, cds_out :: FilePath
                    , default_fwd :: Bool
                    , gen_all :: Bool
                    , fasta,blastx :: FilePath }

options :: [OptDescr (Options -> IO Options)]
options = 
    [ -- Output options
      Option ['R'] ["redir-out"]     (ReqArg (\arg opt -> return (if gen_all opt then incompat
                                                                  else opt { redir_out = arg })) "File") 
                 "File for sequence output,\nreoriented to predicted 5' to 3' direction."
    , Option ['C'] ["cds-out"] (ReqArg (\arg opt -> return opt { cds_out = arg }) "File") 
                 "File for predicted CDS output."
-- todo:
--    , Option ['r'] ["reverse-default"]  (NoArg (\opt -> return opt { default_fwd = False }))
--                 "Reverse sequences without good orientation predictions"

    , Option [] ["all"] (NoArg (\opt -> return (if null (blastx opt) then opt { gen_all = True } 
                                                else incompat))) "Generate all frames"

    -- Input options
    , Option ['i'] ["sequence-file"] (ReqArg (\arg opt -> return opt { fasta = arg }) "File")
                 "File for sequence input (Fasta-format)."
    , Option ['x'] ["blast-xml-file"] (ReqArg (\arg opt -> return (if gen_all opt then incompat
                                                                   else opt { blastx = arg })) "File")
                 "File for Blastx result input\n(XML-format, use 'blastall -m 7')."

    -- Other options
    , Option ['h'] ["help"] (NoArg (\_ -> normalUsage)) "Print usage information."
    ]
        where incompat = error "'--all' is incompatible with '-x' and '-R'."

defaultopts :: Options
defaultopts = Opts { redir_out = "" 
                   , cds_out   = ""
                   , default_fwd = True
                   , gen_all = False
                   , fasta = error "No sequence input specified"
                   , blastx = ""
                   }

parseargs :: [Options -> IO Options] -> IO Options
parseargs args = foldl (>>=) (return defaultopts) args >>= verify
    where verify = return . id