{-# LANGUAGE RecordWildCards #-}
{-# LANGUAGE DeriveDataTypeable #-}
-- | Select Sequences
-- Testcommand: SelectSequences -i /path/to/test.clustal
module Main where
import Control.Monad
import System.Console.CmdArgs
import Bio.SelectSequencesLibrary
import Data.Either.Unwrap
import System.Directory
data Options = Options
{ inputClustalPath :: String,
outputPath :: String,
toogleExternalSelectSequences :: Bool,
seqenceNumber :: Int,
optimalIdentity :: Double,
maximalIdenity :: Double,
referenceSequence :: Bool,
distanceMatrixPath :: String,
reformatIdOption :: String
} deriving (Show,Data,Typeable)
options :: Options
options = Options
{ inputClustalPath = def &= name "c" &= help "Path to input clustal file",
outputPath = def &= name "o" &= help "Path to output directory. Default: current working directory",
toogleExternalSelectSequences = False &= name "e" &= help "Use only replacement of alignment characters and external 'selectSequence.pl'. Default: False",
seqenceNumber = (6 :: Int) &= name "n" &= help "Number of sequences in the output alignment. (Default: 6)",
optimalIdentity = (80 :: Double) &= name "i" &= help "Optimize for this percentage of mean pairwise identity (Default: 80)",
maximalIdenity = (95 :: Double) &= name "m" &= help "Sequences with a higher percentage of pairwise Identity will be removed. (Default: 95)",
referenceSequence = True &= name "x" &= help "The first sequence (=reference sequence) is always present in the output alignment per default. Default: True",
distanceMatrixPath = "" &= name "d" &= help "Path to distance matrix output file, only internal for interal sequence selection, e.g. /home/user/distmat (Default: )",
reformatIdOption = "RNAcode" &= name "r" &= help "Defines how sequence id is reformated, e.g. fitting for RNAcode or not (Default: RNAcode)"
} &= summary "SelectSequences" &= help "Florian Eggenhofer 2016-2018" &= verbosity
main :: IO ()
main = do
Options{..} <- cmdArgs options
currentWorkDirectory <- getCurrentDirectory
let selectedOutputPath = if null outputPath then currentWorkDirectory else outputPath
if toogleExternalSelectSequences
then do
resultStatus <- preprocessClustalForRNAzExternal inputClustalPath (selectedOutputPath ++ "/") seqenceNumber (truncate optimalIdentity) (truncate maximalIdenity) referenceSequence
if isRight resultStatus
then do
let (idMatrix,_) = fromRight resultStatus
return ()
Control.Monad.unless (null distanceMatrixPath) (writeFile distanceMatrixPath idMatrix)
else print ("A problem occured selecting sequences: " ++ fromLeft resultStatus)
else do
resultStatus <- preprocessClustalForRNAz inputClustalPath (selectedOutputPath ++ "/") seqenceNumber optimalIdentity maximalIdenity referenceSequence reformatIdOption
if isRight resultStatus
then do
return ()
else print ("A problem occured selecting sequences: " ++ fromLeft resultStatus)