BiobaseXNA 0.7.0.0 → 0.7.0.1

raw patch · 2 files changed

+61/−1 lines, 2 filesdep +cmdargsnew-component:exe:SubOptDistancePVP ok

version bump matches the API change (PVP)

Dependencies added: cmdargs

API changes (from Hackage documentation)

Files

• BiobaseXNA.cabal +9/−1
• SubOptDistance.hs +52/−0

@@ -1,5 +1,5 @@ name:           BiobaseXNA-version:        0.7.0.0+version:        0.7.0.1 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/@@ -72,6 +72,14 @@    ghc-options:     -O2 -funbox-strict-fields++executable SubOptDistance+  build-depends:+    cmdargs >= 0.10+  main-is:+    SubOptDistance.hs+  ghc-options:+    -O2  source-repository head   type: git

@@ -0,0 +1,52 @@+{-# LANGUAGE ScopedTypeVariables #-}+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE NoMonomorphismRestriction #-}++module Main where++import System.Console.CmdArgs+import Control.Arrow+import Data.Char (isSpace)+import Data.List+import Data.Ord+import Text.Printf++import Biobase.Secondary.Diagrams+import Biobase.Secondary++++data Options = Options+  { structure :: String+  , aq :: Bool+  , qa :: Bool+  } deriving (Show,Data,Typeable)++options = Options+  { structure = "" &= args+  , aq = True &= help "perform target \\\\ query calculation"+  , qa = True &= help "perform query \\\\ target calculation"+  } &= help helpLines++helpLines = unlines+  [ "This program reads a bunch of RNAsubopt lines on STDIN. Provide an"+  , "additional structure as the argument line. The result will be the"+  , "sub-optimal line with lowest base pair distance to the query line."+  ]++main = do+  Options{..} <- cmdArgs options+  (sqn:xs') <- fmap lines $ getContents+  let xs = map (\(s,e) -> (s,dotBracket ["()"] s,read e)) $ map (break isSpace) xs'+  let q = dotBracket ["()"] structure+  let (d,x,e) = getMinimalDistance aq qa q xs+  let distance :: Double = e - ((/100) . read $ words sqn !! 1)+  printf "%4d %s %8.2f %8.2f\n" d x e distance++getMinimalDistance :: Bool -> Bool -> [PairIdx] -> [(String,[PairIdx],Double)] -> (Int,String,Double)+getMinimalDistance aq qa q xs = g $ minimumBy (comparing f) xs where+  g (a,b,c) = ( fst $ f (a,b,c) , a, c)+  f (_,a,e) = (length $ aqs ++ qas , e) where+    aqs = if aq then a \\ q else []+    qas = if qa then q \\ a else []