CMVisualisation.hs

{-# LANGUAGE DeriveDataTypeable #-}
{-# LANGUAGE NoMonomorphismRestriction #-}
{-# LANGUAGE RecordWildCards #-}
{-# LANGUAGE RankNTypes #-}
{-# LANGUAGE FlexibleContexts #-}

-- | Visualize Infernal Covariance Models
--   Datastructures and parsing of covariance models is provided by Biobase
--   Visualization is accomplished with diagrams-svg
--   For more information on Infernal consult <http://eddylab.org/infernal/>

module Main where

import Bio.CMDraw
import qualified Biobase.SElab.CM as CM
import Biobase.SElab.CM.Import (cmFromFile)
import System.Console.CmdArgs
import System.Directory
import Data.Either.Unwrap
import qualified Bio.StockholmParser as SP
import qualified Data.Text as T
import Paths_cmv (version)
import Data.Version (showVersion)
import Data.List (intercalate)
import Control.Monad
import Data.Maybe

options :: Options
data Options = Options
  { modelFile :: String,
    alignmentFile :: String,
    modelDetail :: String,
    modelLayout :: String,
    emissionLayout :: String,
    alignmentEntries :: Int,
    transitionCutoff :: Double,
    maxWidth :: Double,
    scalingFactor :: Double,
    outputFormat :: String,
    outputDirectoryPath :: String,
    secondaryStructureVisTool :: String,
    modelNameToggle :: Bool
  } deriving (Show,Data,Typeable)

options = Options
  { modelFile = def &= name "m" &= help "Path to covariance model file",
    alignmentFile = "" &= name "s" &= help "Path to stockholm alignment file",
    modelDetail = "detailed" &= name "d" &= help "Set verbosity of drawn models: minimal, simple, detailed",
    modelLayout = "tree" &= name "l" &= help "Set layout of drawn models: flat, tree",
    emissionLayout = "box" &= name "e" &= help "Set layout of drawn models: score, probability, box (Default: box)",
    alignmentEntries = (50 :: Int) &= name "n" &= help "Set cutoff for included stockholm alignment entries (Default: 50)",
    transitionCutoff = (0.01 :: Double) &= name "t" &= help "Minimal value for a transition probability to be displayed (Default: 0.01)",
    maxWidth = (200 :: Double) &= name "w" &= help "Set maximal width of result figure (Default: 100)",
    scalingFactor = (2.0 :: Double) &= name "c" &= help "Set uniform scaling factor for image size (Default: 2)",
    outputFormat = "pdf" &= name "f" &= help "Output image format: pdf, svg, png, ps (Default: pdf)",
    outputDirectoryPath = "" &= name "p" &= help "Output directory path (Default: none)",
    secondaryStructureVisTool = "" &= name "x" &= help "Select tool for secondary structure visualisation: forna, r2r (Default: none)",
    modelNameToggle = False  &= name "b" &= help "Write all comma separted model names to modelNames file (Default: False)"
  } &= summary ("CMV " ++ toolVersion) &= help "Florian Eggenhofer - 2013-2016" &= verbosity

main :: IO ()
main = do
  Options{..} <- cmdArgs options
  modelFileExists <- doesFileExist modelFile
  if modelFileExists
    then do
      cms <- cmFromFile modelFile
      if not (null cms)
        then do
          alnInput <- SP.readExistingStockholm alignmentFile
          Control.Monad.when (isLeft alnInput) $ print (fromLeft alnInput)
          --let outputName = diagramName "cmv" outputFormat
          let modelNumber = length cms
          let alns = if isRight alnInput then map (\a -> Just a) (fromRight alnInput) else replicate modelNumber Nothing
          let currentModelNames = map (T.unpack . CM._name) cms
          currentWD <- getCurrentDirectory
          let dirPath = if null outputDirectoryPath then currentWD else outputDirectoryPath
          writeModelNameFile modelNameToggle dirPath currentModelNames
          let modelFileNames = map (\m -> m ++ "." ++ outputFormat) currentModelNames
          let alignmentFileNames = map (\m -> m ++ ".aln" ++ "." ++ outputFormat) currentModelNames
          setCurrentDirectory dirPath
          let (modelVis,alignmentVis)= unzip $ drawSingleCMs modelDetail alignmentEntries transitionCutoff modelLayout emissionLayout maxWidth scalingFactor cms alns
          mapM_ (\(a,b) -> printCM a svgsize b) (zip modelFileNames modelVis)
          mapM_ (\(alnPath,stockholm) -> if isJust stockholm then printCM alnPath svgsize (fromJust stockholm) else return ()) (zip alignmentFileNames alignmentVis)
          let structureVisType = "perModel"
          if structureVisType == "perModel"
            then do
              let structureFilePath = dirPath ++ "/"
              let structureVisInputs = perModelSecondaryStructureVisualisation secondaryStructureVisTool maxWidth structureFilePath cms alns []
              mapM_ (\(structureFileName,structureVis) -> writeFile structureFileName structureVis) structureVisInputs
              setCurrentDirectory currentWD
            else do
              let structureFilePaths = map (\m -> dirPath ++ "/" ++ m ++ "." ++ secondaryStructureVisTool) currentModelNames
              let structureVisInputs = mergedSecondaryStructureVisualisation secondaryStructureVisTool maxWidth cms alns []
              mapM_ (\(structureFileName,(structureVis,_)) -> writeFile structureFileName structureVis) (zip structureFilePaths structureVisInputs)
              mapM_ (\(structureFileName,(_,colorScheme)) -> writeFile (structureFileName ++"Color") colorScheme) (zip structureFilePaths structureVisInputs)
              setCurrentDirectory currentWD
          
        else
          print "Could not read covariance models from input file"
    else
      putStrLn "Input model file not found"

toolVersion :: String
toolVersion = showVersion version

writeModelNameFile :: Bool -> String -> [String] -> IO ()
writeModelNameFile toggle outputDirectoryPath modelNames =
  if toggle
    then do
       let modelNamesString = intercalate "," modelNames
       writeFile (outputDirectoryPath ++ "modelNames") modelNamesString
    else return ()