diff --git a/CMCompare.cabal b/CMCompare.cabal new file mode 100644 --- /dev/null +++ b/CMCompare.cabal @@ -0,0 +1,39 @@ +name: CMCompare +version: 0.0.1.1 +author: Christian Hoener zu Siederdissen, Ivo L. Hofacker +maintainer: choener@tbi.univie.ac.at +copyright: Christian Hoener zu Siederdissen, Ivo L. Hofacker, 2010 +homepage: http://www.tbi.univie.ac.at/software/cmcompare/ +category: Bioinformatics +synopsis: Infernal covariance model comparison +license: GPL-3 +license-file: LICENSE +build-type: Simple +stability: experimental +cabal-version: >= 1.4.0 +description: + Compares two Infernal covariance models. Returns the common + MaxiMin score and the offending RNA sequence. High scores point + toward low discriminative power of the two models. Based on: + "Discriminatory Power or RNA Family Models, Hoener zu + Siederdissen and Hofacker, 2010, accepted for eccb10" + +extra-source-files: + scripts/HighScoreEdges.sh + scripts/NeighborGraph.sh + +executable hsCMCompare + build-depends: + base >= 4 && < 5, + cmdargs == 0.3, + array, + + Biobase >= 0.0.2 && < 0.0.3, + BiobaseInfernal >= 0.0.2 && < 0.0.3, + HsTools >= 0.0.1.1 && < 0.0.2 + + main-is: + CMCompare.hs + + ghc-options: + -O2 diff --git a/CMCompare.hs b/CMCompare.hs new file mode 100644 --- /dev/null +++ b/CMCompare.hs @@ -0,0 +1,447 @@ +{-# LANGUAGE StandaloneDeriving #-} +{-# LANGUAGE RecordWildCards #-} +{-# LANGUAGE DeriveDataTypeable #-} + +-- Based on: Discriminatory Power of RNA Family Models, Christian Hoener zu +-- Siederdissen and Ivo Hofacker, 2010, accepted for eccb10: +-- +-- Preprint: +-- +-- http://www.tbi.univie.ac.at/newpapers/abstracts/abstractTBI-p-2010-5.html + + + +-- NOTE always use coverage analysis to find out, if we really used all code +-- paths (in long models, if a path is not taken, there is a bug) + +-- NOTE when comparing hits with cmsearch, use the following commandline: +-- +-- cmsearch --no-null3 --cyk --fil-no-hmm --fil-no-qdb +-- +-- --no-null3 : important, the test sequence is so short that null3 can easily +-- generate scores that are way off! remember, we are interested in a sequence +-- that is typically embedded in something large +-- +-- --fil-no-hmm, --fil-no-qdb: do not use heuristics for speedup, they +-- sometimes hide results (in at least one case) +-- +-- (--toponly): if the comparison was done onesided +-- +-- (-g): if you want to compare globally + +-- {{{ module descriptor + +module Main where + +import Data.Array.IArray +import Text.Printf +import Control.Monad +import Debug.Trace +import System.Environment (getArgs) +import System.Console.CmdArgs +import Data.List (maximumBy,nub,sort) +import Control.Arrow (first,second,(***)) + +import Biobase.Infernal.CM +import Biobase.Infernal.CM.Import +import Biobase.RNA hiding (nucE) +import qualified Biobase.RNA as RNA +import Debug.Trace.Tools + +-- }}} + +-- * optimization functions + +-- {{{ type of the optimization functions + +type StateID = Int -- TODO should this go into BiobaseCM? +type CM' = CM () () + +type Opt a = + ( CM' -> StateID -> a -- E + , CM' -> StateID -> Double -> a -> a -- lbegin + , CM' -> StateID -> Double -> a -> a -- S + , CM' -> StateID -> Double -> a -> a -- D + , CM' -> StateID -> Double -> Emission -> a -> a -- MP + , CM' -> StateID -> Double -> Emission -> a -> a -- ML + , CM' -> StateID -> Double -> Emission -> a -> a -- IL + , CM' -> StateID -> Double -> Emission -> a -> a -- MR + , CM' -> StateID -> Double -> Emission -> a -> a -- IR + , CM' -> StateID -> a -> a -> a -- B + , [(a,a)] -> [(a,a)] -- optimization + , a -> String -- finalize, make pretty for output + ) + +-- }}} + +-- {{{ optimization functions + +-- | calculates the cyk optimal score over both models. + +cykMaxiMin :: Opt Double +cykMaxiMin = (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) where + end _ _ = 0 + lbegin _ _ t s = t + s + start _ _ t s = t + s + delete _ _ t s = t + s + matchP _ _ t (EmitP _ _ e) s = t + e + s + matchL _ _ t (EmitS _ e) s = t + e + s + insertL _ _ t (EmitS _ e) s = t + e + s + matchR _ _ t (EmitS _ e) s = t + e + s + insertR _ _ t (EmitS _ e) s = t + e + s + branch _ _ s t = s + t + opt [] = [] + opt xs = [maximumBy (\(a,b) (c,d) -> (min a b) `compare` (min c d)) xs] + finalize s = show s + +-- | return the nucleotide sequence leading to the score. uses an optional +-- endmarker to denote end states. the string is the same for both models. this +-- is the only Opt function, currently, for which this is true. + +rnaString :: Bool -> Opt [Nucleotide] +rnaString endmarker = (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) where + end _ _ = [RNA.nucE | endmarker] + lbegin _ _ _ s = s + start _ _ _ s = s + delete _ _ _ s = s + matchP _ _ _ (EmitP k1 k2 _) s = [k1] ++ s ++ [k2] + matchL _ _ _ (EmitS k _) s = k : s + insertL _ _ _ (EmitS k _) s = k : s + matchR _ _ _ (EmitS k _) s = s ++ [k] + insertR _ _ _ (EmitS k _) s = s ++ [k] + branch _ _ s t = s ++ t + opt = id + finalize s = if endmarker + then concatMap f s + else concatMap show s + f x + | x==RNA.nucE = "_" + | otherwise = show x + +-- | dotbracket notation, again with an endmarker, to see the secondary +-- structure corresponding to the rnastring. + +dotBracket :: Bool -> Opt String +dotBracket endmarker = (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) where + end _ _ = ['_' | endmarker] + lbegin _ _ _ s = s + start _ _ _ s = s + delete _ _ _ s = s + matchP _ _ _ _ s = "(" ++ s ++ ")" + matchL _ _ _ _ s = '.' : s + insertL _ _ _ _ s = ',' : s + matchR _ _ _ _ s = s ++ "." + insertR _ _ _ _ s = s ++ "," + branch _ _ s t = s ++ t + opt = id + finalize s = s + +-- | show the nodes which were visited to get the score. the last node can +-- occur multiple times. if it does, local end transitions were used. + +visitedNodes :: Opt [Int] +visitedNodes = (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) where + end cm k = [snode (states cm ! k)] + lbegin cm k _ s = s + start cm k _ s = snode (states cm ! k) : s + delete cm k _ s = snode (states cm ! k) : s + matchP cm k _ _ s = snode (states cm ! k) : s + matchL cm k _ _ s = snode (states cm ! k) : s + insertL cm k _ _ s = snode (states cm ! k) : s + matchR cm k _ _ s = snode (states cm ! k) : s + insertR cm k _ _ s = snode (states cm ! k) : s + branch cm k s t = snode (states cm ! k) : (s ++ t) + opt = id -- NOTE do not sort, do not nub ! + finalize xs = "Nodes: " ++ show xs -- NOTE do not sort, do not nub ! + +-- | detailed output of the different states, that were visited. + +extendedOutput :: Opt String +extendedOutput = (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) where + end cm sid = printf "E %5d %5d" sid (snode (states cm ! sid)) + lbegin cm sid t s = printf "lbegin %5d %5d %7.3f \n%s" sid (snode (states cm ! sid)) t s + start cm sid t s = printf "S %5d %5d %7.3f \n%s" sid (snode (states cm ! sid)) t s + delete cm sid t s = printf "D %5d %5d %7.3f \n%s" sid (snode (states cm ! sid)) t s + matchP cm sid t (EmitP k1 k2 e) s = printf "MP %5d %5d %7.3f %7.3f %1s %1s\n%s" sid (snode (states cm ! sid)) t e (show k1) (show k2) s + matchL cm sid t (EmitS k e) s = printf "ML %5d %5d %7.3f %7.3f %1s\n%s" sid (snode (states cm ! sid)) t e (show k) s + insertL cm sid t (EmitS k e) s = printf "IL %5d %5d %7.3f %7.3f %1s\n%s" sid (snode (states cm ! sid)) t e (show k) s + matchR cm sid t (EmitS k e) s = printf "MR %5d %5d %7.3f %7.3f %1s\n%s" sid (snode (states cm ! sid)) t e (show k) s + insertR cm sid t (EmitS k e) s = printf "IR %5d %5d %7.3f %7.3f %1s\n%s" sid (snode (states cm ! sid)) t e (show k) s + branch cm sid s t = printf "B %5d %5d\n%s\n%s" sid (snode (states cm ! sid)) s t + opt = id + finalize s = "\nLabel State Node Trans Emis\n\n" ++ s + +(<*>) :: Eq a => Opt a -> Opt b -> Opt (a,b) +algA <*> algB = (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) where + (endA,lbeginA,startA,deleteA,matchPA,matchLA,insertLA,matchRA,insertRA,branchA,optA,finalizeA) = algA + (endB,lbeginB,startB,deleteB,matchPB,matchLB,insertLB,matchRB,insertRB,branchB,optB,finalizeB) = algB + end cm k = (endA cm k, endB cm k) + lbegin cm k t (sA,sB) = (lbeginA cm k t sA, lbeginB cm k t sB) + start cm k t (sA,sB) = (startA cm k t sA, startB cm k t sB) + delete cm k t (sA,sB) = (deleteA cm k t sA, deleteB cm k t sB) + matchP cm k t e (sA,sB) = (matchPA cm k t e sA, matchPB cm k t e sB) + matchL cm k t e (sA,sB) = (matchLA cm k t e sA, matchLB cm k t e sB) + insertL cm k t e (sA,sB) = (insertLA cm k t e sA, insertLB cm k t e sB) + matchR cm k t e (sA,sB) = (matchRA cm k t e sA, matchRB cm k t e sB) + insertR cm k t e (sA,sB) = (insertRA cm k t e sA, insertRB cm k t e sB) + branch cm k (sA,sB) (tA,tB) = (branchA cm k sA tA, branchB cm k sB tB) + opt xs = [((xl1,xl2),(xr1,xr2)) | (xl1,xr1) <- nub $ optA [(yl1,yr1) | ((yl1,yl2),(yr1,yr2)) <- xs] + , (xl2,xr2) <- optB [(yl2,yr2) | ((yl1,yl2),(yr1,yr2)) <- xs, (yl1,yr1) == (xl1,xr1)] + ] + finalize (sA,sB) = finalizeA sA ++ "\n" ++ finalizeB sB + +-- }}} + +-- * recursion in two CMs simultanously + +-- {{{ main recursion + +recurse :: Opt a -> CM' -> CM' -> Array (Int,Int) [(a,a)] +recurse (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) m1 m2 = locarr where + + loc k1 k2 + | cmType m1 == CMProb || cmType m2 == CMProb = error "both models need to be score type models" + | otherwise = opt $ do + r <- arr ! (k1, k2) + return $ (lbegin m1 k1 lb1 *** lbegin m2 k2 lb2) r + where + lb1 = localBegin m1 ! k1 + lb2 = localBegin m2 ! k2 + + rec k1 k2 + -- + | t1 == E && t2 == E = [(end m1 k1, end m2 k2)] + -- + | t1 == S && t2 == S = opt $ do + Transition c1 tr1 <- schildren s1 ++ [Transition ls1 le1 | acceptLE le1] + Transition c2 tr2 <- schildren s2 ++ [Transition ls2 le2 | acceptLE le2] + r <- arr ! (c1, c2) + return $ (start m1 k1 tr1 *** start m2 k2 tr2) r + | t1 == D && t2 == D = opt $ do + Transition c1 tr1 <- schildren s1 ++ [Transition ls1 le1 | acceptLE le1] + Transition c2 tr2 <- schildren s2 ++ [Transition ls2 le2 | acceptLE le2] + r <- arr ! (c1, c2) + return $ (delete m1 k1 tr1 *** delete m2 k2 tr2) r + -- match pair emitting states + | t1 == MP && t2 == MP + = opt $ do + Transition c1 tr1 <- schildren s1 ++ [Transition ls1 le1 | acceptLE le1] + Transition c2 tr2 <- schildren s2 ++ [Transition ls2 le2 | acceptLE le2] + (e1,e2) <- zip (semission s1) (semission s2) + r <- arr ! (c1, c2) + return $ (matchP m1 k1 tr1 e1 *** matchP m2 k2 tr2 e2) r + -- match left emitting states + | t1 `elem` lstates && t2 `elem` lstates + = opt $ do + Transition c1 tr1 <- schildren s1 ++ [Transition ls1 le1 | acceptLE le1] + Transition c2 tr2 <- schildren s2 ++ [Transition ls2 le2 | acceptLE le2] + guard $ c1 /= k1 || c2 /= k2 + (e1,e2) <- zip (semission s1) (semission s2) + r <- arr ! (c1, c2) + let f = if t1 == ML then matchL else insertL + let g = if t2 == ML then matchL else insertL + return $ (f m1 k1 tr1 e1 *** g m2 k2 tr2 e2) r + -- match right emitting states + | t1 `elem` rstates && t2 `elem` rstates + = opt $ do + Transition c1 tr1 <- schildren s1 ++ [Transition ls1 le1 | acceptLE le1] + Transition c2 tr2 <- schildren s2 ++ [Transition ls2 le2 | acceptLE le2] + guard $ c1 /= k1 || c2 /= k2 + (e1,e2) <- zip (semission s1) (semission s2) + r <- arr ! (c1, c2) + let f = if t1 == MR then matchR else insertR + let g = if t2 == MR then matchR else insertR + return $ (f m1 k1 tr1 e1 *** g m2 k2 tr2 e2) r + -- if one state is E, we can only delete states, except for another S state, which will go into local end + -- it is not possible to use an emitting state on the right as those would require emitting on the left, too! + | t1 == E && t2 `elem` [D,S] = opt $ do + Transition c2 tr2 <- schildren s2 ++ [Transition ls2 le2 | acceptLE le2] + r <- arr ! (k1,c2) + return $ if t2 == D then second (delete m2 k2 tr2) r else second (start m2 k2 tr2) r + -- the other way around with D,E + | t1 `elem` [D,S] && t2 == E = opt $ do + Transition c1 tr1 <- schildren s1 ++ [Transition ls1 le1 | acceptLE le1] + r <- arr ! (c1,k2) + return $ if t1 == D then first (delete m1 k1 tr1) r else first (start m1 k1 tr1) r + -- two branching states + | t1 == B && t2 == B = opt $ + let + [Branch l1, Branch r1] = schildren s1 + [Branch l2, Branch r2] = schildren s2 + in + -- both branches are matched + do + (s1,s2) <- arr ! (l1,l2) -- left branch (m1,m2) + (t1,t2) <- arr ! (r1,r2) -- right branch (m1,m2) + return (branch m1 k1 s1 t1, branch m2 k2 s2 t2) -- (m1,m2) + ++ + do + (t1,s2) <- arr ! (r1,l2) -- match right branch of m1 with left branch of m2 + -- local ends for other branches + x <- arr ! (ls1,ls2) + let (s1,t2) = (delete m1 l1 le1 *** delete m2 l2 le2) x + return (branch m1 k1 s1 t1, branch m2 k2 s2 t2) + ++ + do + (s1,t2) <- arr ! (l1,r2) + x <- arr ! (ls1,ls2) + let (t1,s2) = (delete m1 l1 le1 *** delete m2 l2 le2) x + return (branch m1 k1 s1 t1, branch m2 k2 s2 t2) + -- branch - non-branch + | t1 == B && t2 /= B = opt $ + let + [Branch l, Branch r] = schildren s1 + in + do + (s1,s2) <- arr ! (l,k2) -- left branch and m2 + x <- arr ! (ls1,ls2) + -- dont do anything for ls2, since we do not have to + -- delete a branch in model 2. + let (t1,t2) = first (delete m1 r le1) x + return (branch m1 k1 s1 t1, branch m2 k2 s2 t2) + ++ + do + (t1,t2) <- arr ! (r,k2) -- right branch and m2 + x <- arr ! (ls1,ls2) + let (s1,s2) = first (delete m1 l le1) x -- delete left branch in m1 + return (branch m1 k1 s1 t1, branch m2 k2 s2 t2) + -- branch - non-branch + | t1 /= B && t2 == B = opt $ + let + [Branch l, Branch r] = schildren s2 + in + do + (s1,s2) <- arr ! (k1,l) + x <- arr ! (ls1,ls2) + let (t1,t2) = second (delete m2 r le2) x + return (branch m1 k1 s1 t1, branch m2 k2 s2 t2) + ++ + do + (t1,t2) <- arr ! (k1,r) + x <- arr ! (ls1,ls2) + let (s1,s2) = second (delete m2 l le2) x + return (branch m1 k1 s1 t1, branch m2 k2 s2 t2) + -- S state versus any + | t1 == S = opt $ do + Transition c1 tr1 <- schildren s1 ++ [Transition ls1 le1 | acceptLE le1] + r <- arr ! (c1, k2) + return $ first (start m1 k1 tr1) r + -- S state versus any + | t2 == S = opt $ do + Transition c2 tr2 <- schildren s2 ++ [Transition ls2 le2 | acceptLE le2] + r <- arr ! (k1, c2) + return $ second (start m2 k2 tr2) r + -- + | otherwise = [] + where + s1 = states m1 ! k1 + s2 = states m2 ! k2 + t1 = stype s1 + t2 = stype s2 + le1 = localEnd m1 ! k1 + le2 = localEnd m2 ! k2 + ls1 = snd . bounds $ states m1 -- last state (E) + ls2 = snd . bounds $ states m2 + lstates = [ML,IL] + rstates = [MR,IR] + acceptLE x + | cmType m1 == CMScore && x > (-1/0) = True + | cmType m1 == CMProb && x /= 0 = True + | otherwise = False + + locarr = (array ((0,0),(sn1,sn2)) [((k1,k2),loc k1 k2) | k1 <- [0 .. sn1], k2 <- [0 .. sn2]]) `asTypeOf` arr + arr = (array ((0,0),(sn1,sn2)) [((k1,k2),rec k1 k2) | k1 <- [0 .. sn1], k2 <- [0 .. sn2]]) `asTypeOf` locarr + (_,sn1) = bounds $ states m1 + (_,sn2) = bounds $ states m2 + +-- }}} + +-- {{{ main + +-- TODO add an option to filter by minimal score (default: -1000000) if the +-- filter is on, we get a result only, if the score is above the threshold + +data Options = Options + { global :: Bool + , invert :: Bool + , pbegin :: Double + , pend :: Double + , endmarker :: Bool + , nobeginilir :: Bool + , models :: [String] + } deriving (Show,Data,Typeable) + +options = Options + { global = False &= help "global model comparison" + , invert = False &= help "TODO invert second model (read right to left)" + , pbegin = 0.05 &= help "aggregate local begin probability" + , pend = 0.05 &= help "aggregate local end probability" + , endmarker = False &= help "add an endmarker into the rnastring to denote local ends" + , nobeginilir = False &= help "trailing left or right nucleotides change the score" + , models = def &= args &= help "path to exactly two covariance models" + } &= summary "CMCompare: Discriminatory Power of RNA Family Models\n(c) 2010, Christian Hoener zu Siederdissen and Ivo Hofacker\nchoener@tbi.univie.ac.at\nLicensed under the GPLv3\n" +-- TODO put fixTransition in BiobaseInfernal, rename and whatnot + +-- | what is this? this sets the transition score in the root to 0 for the +-- transition into IL and IR. For CM comparison, this makes sense. Consider two +-- cms .(.) and (.); given "acag" both should score about the same, but the +-- second can only, if IL eats a nucleotide. for single CM search, this is +-- taken care of by the DP algorithm which doesn't work here. + +fixTransition :: CM' -> CM' +fixTransition x = x{states = ss // [(0,rtnew)]} where + ss = states x + rt = ss ! 0 + tr = schildren rt + trnew = [Transition 1 0, Transition 2 0] ++ drop 2 tr + rtnew = rt{schildren = trnew} + +applyIf c f = if c then f else id + +answers optf m1 m2 = map (finalize *** finalize) . opt . concat . elems $ recurse optf m1 m2 where + (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) = optf + +results optf m1 m2 = opt . concat . elems $ recurse optf m1 m2 where + (end,lbegin,start,delete,matchP,matchL,insertL,matchR,insertR,branch,opt,finalize) = optf + +main = do + Options{..} <- cmdArgs options + normal <- isNormal + loud <- isLoud + let quiet = not normal + unless (length models == 2) $ do + fail "give exactly two CMs" + let [a,b] = models + Right [m1'] <- fromFile a + Right [m2'] <- fromFile b + let m1 = applyIf (not nobeginilir) fixTransition $ applyIf (not global) (cmMakeLocal pbegin pend) m1' + let m2 = applyIf (not nobeginilir) fixTransition $ applyIf (not global) (cmMakeLocal pbegin pend) m2' + let pr = (\(x,y) -> putStrLn x >> putStrLn "" >> putStrLn y >> putStrLn "++++++++++++") + when (quiet && not normal) $ do + let (a1,a2) = head $ results cykMaxiMin m1 m2 + printf "%s %s %10.3f %10.3f\n" a b a1 a2 + when (normal && not loud) $ do + let ((((cyk1,vn1),rna1),db1),(((cyk2,vn2),_),db2)) = head $ results (cykMaxiMin <*> visitedNodes <*> rnaString endmarker <*> dotBracket endmarker) m1 m2 + let rnaBoth = concatMap f rna1 where + f x + | x==RNA.nucE = "_" + | otherwise = show x + printf "%s %s %10.3f %10.3f %s %s %s %s %s\n" a b cyk1 cyk2 rnaBoth db1 db2 (show vn1) (show vn2) + when loud . mapM_ pr $ answers (cykMaxiMin <*> visitedNodes <*> rnaString endmarker <*> dotBracket endmarker <*> extendedOutput) m1 m2 + +-- }}} + +-- * Helper functions + +-- {{{ + +-- | summation in logspace + +-- TODO time for a new library ;) + +logSum x y = h + log (1 + exp (l-h)) where + h = max x y + l = min x y + +-- }}} + diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,675 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. + diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,2 @@ +import Distribution.Simple +main = defaultMain diff --git a/scripts/HighScoreEdges.sh b/scripts/HighScoreEdges.sh new file mode 100644 --- /dev/null +++ b/scripts/HighScoreEdges.sh @@ -0,0 +1,34 @@ +#! /bin/bash + +# Christian Hoener zu Siederdissen, 2010 +# choener@tbi.univie.ac.at +# Distributed "as-is" without any warranty + +# Generate a graph of high-scoring edges between nodes. This script does not +# check parameters before using them. This is mostly because no operation +# writes or deletes anything. All results go to stdout! + +# The following parameters are required: +# 1. directory containing Rfam models +# 2. number of edges to generate +# x. input is stdin, with (1) model name (2) model name (3) score + +# Everything is then wrapped for graphviz dot output: +# zcat rfam-weakpairs.gz | HighScoreEdges.sh ../Rfam 200 | dot -Tps > graph.ps + +repWithName () { + NUM1=`echo $2 | grep -o "[0-9]*"` + NUM2=`echo $3 | grep -o "[0-9]*"` + NAME1=`cat $1/RF$NUM1.cm | grep NAME | awk '{print $2}'` + NAME2=`cat $1/RF$NUM2.cm | grep NAME | awk '{print $2}'` + W=`echo $4 | awk '{printf "%d", $1}'` + echo "\"$NUM1\n$NAME1\" -- \"$NUM2\n$NAME2\" [label = \"$W\"];" +} + +echo "graph g {" + +tail -n$2 | while read line ; do + repWithName $1 $line +done | sort + +echo "}" diff --git a/scripts/NeighborGraph.sh b/scripts/NeighborGraph.sh new file mode 100644 --- /dev/null +++ b/scripts/NeighborGraph.sh @@ -0,0 +1,35 @@ +#! /bin/bash + +# Christian Hoener zu Siederdissen, 2010 +# choener@tbi.univie.ac.at +# Distributed "as-is" without any warranty + +# Generate a graph of the high-scoring neighborhood of a single Rfam family. +# This script does not check parameters before using them. This is mostly +# because no operation writes or deletes anything. All results go to stdout! + +# The following parameters are required: +# 1. directory containing Rfam models +# 2. model for which neighbors are to be generated +# 3. number of edges to generate +# x. input is stdin, with (1) model name (2) model name (3) score + +# Everything is then wrapped for graphviz dot output: +# zcat rfam-weakpairs.gz | NeighborGraph.sh ../Rfam RF00943 10 | circo -Tps > graph.ps + +repWithName () { + NUM1=`echo $2 | grep -o "[0-9]*"` + NUM2=`echo $3 | grep -o "[0-9]*"` + NAME1=`cat $1/RF$NUM1.cm | grep NAME | awk '{print $2}'` + NAME2=`cat $1/RF$NUM2.cm | grep NAME | awk '{print $2}'` + W=`echo $4 | awk '{printf "%d", $1}'` + echo "\"$NUM1\n$NAME1\" -- \"$NUM2\n$NAME2\" [label = \"$W\"];" +} + +echo "graph g {" + +grep $2 | tail -n$3 | while read line ; do + repWithName $1 $line +done | sort + +echo "}"