BiobaseInfernal (empty) → 0.0.2.0

raw patch · 8 files changed

+1360/−0 lines, 8 filesdep +Biobasedep +arraydep +basesetup-changed

Dependencies added: Biobase, array, base, containers, parsec

Files

• Biobase/Infernal/CM.hs +326/−0
• Biobase/Infernal/CM/Export.hs +76/−0
• Biobase/Infernal/CM/Import.hs +194/−0
• Biobase/Infernal/Stockholm.hs +16/−0
• Biobase/Infernal/Stockholm/Import.hs +35/−0
• BiobaseInfernal.cabal +36/−0
• LICENSE +675/−0
• Setup.hs +2/−0

@@ -0,0 +1,326 @@++--+-- Stores Infernal Covariance Model data. Built for ease of use, not speed but+-- should work reasonably well.+--++-- TODO Data.Vector?+--+-- TODO use generics?+--+-- TODO functions to change to probabilities!+--+-- TODO cmCanonize function!+--+-- TODO put functions into their own modules, a bit of cleanup+--+-- TODO add functions to insert a new node between two already existing nodes; think about how to handle BIF+--+-- TODO add ability to remove node; think about how to handle BIF+--+-- NOTE maybe BIF should not be insertable/removable right now?++module Biobase.Infernal.CM where+++import Data.Array.IArray+import Data.List (genericLength)++import Biobase.RNA hiding (nucE) -- "E type" nucleotides do not happen in CMs!++++-- * Data types for Covariance Models++-- {{{ Data types++-- | A complete covariance model. Each node and each state can be tagged with+-- additional data. Typically, say after parsing, the tag will be ().++data CM n s = CM+  { nodes      :: Array Int (Node n)+  , states     :: Array Int (State s)+  , header     :: [(String,String)] -- keeps the list of header entries sorted!+  , localBegin :: Array Int Double+  , localEnd   :: Array Int Double+  , cmType     :: CMType+  , nullModel  :: Array Nucleotide Double+  } deriving (Show)++-- | Describes one node++data Node n = Node+  { nid :: Int+  , ntype :: NodeType+  , nparents :: [Int] -- TODO can there be more than one?+  , nchildren :: [Int]+  , nstates :: [Int]+  , ntag :: n+  } deriving (Show)++-- | One state++data State s = State+  { sid :: Int+  , stype :: StateType+  , snode :: Int+  , sparents :: [Int]+  , schildren :: [Transition]+  , semission :: [Emission]+  , stag :: s+  } deriving (Show)++-- | CMType is important if we want to set localBegin / localEnd!++data CMType = CMProb | CMScore+  deriving (Show,Eq)++-- | can emit either one nucleotide or a pair++data Emission+  = EmitS {eNuc :: Nucleotide, escore :: Double}+  | EmitP { eNucL :: Nucleotide, eNucR :: Nucleotide, escore :: Double}+  deriving (Show)++-- | branches are transition without attached probability becaue both branches are always taken++data Transition+  = Branch {tchild :: Int}+  | Transition {tchild :: Int, tscore :: Double}+  deriving (Show)++-- | the different node types++data NodeType = MATP | MATL | MATR | BIF | ROOT | BEGL | BEGR | END+  deriving (Read,Show,Eq,Ord,Enum,Bounded)++-- | the different state types++data StateType = MP | IL | IR | D | ML | MR | B | S | E+  deriving (Read,Show,Eq,Ord,Enum,Bounded)++-- }}}+++-- * make a local model out of a global one++-- | generate a local model with local begin prob and local end prob++cmMakeLocal :: Double -> Double -> CM n s -> CM n s+cmMakeLocal pbegin pend cm = cmMakeLocalBegin pbegin $ cmMakeLocalEnd pend cm++++cmMakeLocalBegin :: Double -> CM n s -> CM n s+cmMakeLocalBegin pbegin cm = cm{localBegin = localBegin cm // changes} where+  changes = rootS : (start : intern)+  rootS = (0, prob2Score 0 1.0) -- root disabled!+  start = (head . nstates $ nodes cm ! 1, prob2Score (1-pbegin) 1.0) -- the first state after "root 0"+  intern = map (\k -> (sid $ nodeMainState cm k,prob2Score (pbegin / l) 1.0)) nds+  nds = filter (localBeginPossible cm) . elems $ nodes cm+  l = genericLength nds++++-- TODO have to change the transition score, too!++cmMakeLocalEnd :: Double -> CM n s -> CM n s+cmMakeLocalEnd pend cm = cm{localEnd = localEnd cm // changes} where+  changes = map (\k -> (sid $ nodeMainState cm k,prob2Score (pend / l) 1.0)) nds+  nds = filter (localBeginPossible cm) . elems $ nodes cm+  l = genericLength nds++++-- * Transform between score and probability mode++-- | given a CM in score mode, change it to probability mode++cmScore2Prob :: CM n s -> CM n s+cmScore2Prob cm' = if cmType cm' == CMProb then cm' else CM+  (nodes  cm)+  (statesScore2Prob cm $ states cm)+  (header cm)+  (localBeginScore2Prob $ localBegin cm)+  (localEndScore2Prob   $ localEnd   cm)+  CMProb+  nm+  where+    nm = amap (flip score2Prob 0.25) $ nullModel cm'+    cm = cm' {nullModel = nm}+++-- | Given a CM in prob mode, change to score mode++cmProb2Score :: CM n s -> CM n s+cmProb2Score cm' = if cmType cm' == CMScore then cm' else CM+  (nodes  cm)+  (statesProb2Score cm $ states cm)+  (header cm)+  (localBeginProb2Score $ localBegin cm)+  (localEndProb2Score   $ localEnd   cm)+  CMScore+  nm+  where+    nm = amap (flip prob2Score 0.25) $ nullModel cm'+    cm = cm' {nullModel = nm}++++-- | normalize all PROBabilities in a CM++cmNormalizeProbabilities :: CM n s -> CM n s+cmNormalizeProbabilities cm+  | cmType cm == CMScore = error "cannot normalize score-type CM"+  | otherwise            = cm -- TODO have to map normalization over all scores!++++-- {{{ CM score/prob conversion helpers++statesScore2Prob :: CM n s -> Array Int (State s) -> Array Int (State s)+statesScore2Prob cm sA = amap f sA where+  f s = s {schildren = map fT $ schildren s, semission = map fE $ semission s}+  fT b@(Branch _) = b+  fT (Transition k v) = Transition k (score2Prob v 1.0)+  fE (EmitS k v) = EmitS k (score2Prob v $ nullModel cm ! k)+  fE (EmitP k1 k2 v) = EmitP k1 k2 (score2Prob v $ (nullModel cm ! k1) * (nullModel cm ! k2))++++localBeginScore2Prob :: Array Int Double -> Array Int Double+localBeginScore2Prob sA = amap f sA where+  f s = score2Prob s 1.0++++localEndScore2Prob :: Array Int Double -> Array Int Double+localEndScore2Prob sA = amap f sA where+  f s = score2Prob s 1.0++++statesProb2Score :: CM n s -> Array Int (State s) -> Array Int (State s)+statesProb2Score cm sA = amap f sA where+  f s = s {schildren = map fT $ schildren s, semission = map fE $ semission s}+  fT b@(Branch _) = b+  fT (Transition k v) = Transition k (prob2Score v 1.0)+  fE (EmitS k v) = EmitS k (prob2Score v $ nullModel cm ! k)+  fE (EmitP k1 k2 v) = EmitP k1 k2 (prob2Score v $ (nullModel cm ! k1) * (nullModel cm ! k2))++++localBeginProb2Score :: Array Int Double -> Array Int Double+localBeginProb2Score sA = amap f sA where+  f s = prob2Score s 1.0++++localEndProb2Score :: Array Int Double -> Array Int Double+localEndProb2Score sA = amap f sA where+  f s = score2Prob s 1.0++-- }}}+++++-- * Helper Functions++-- {{{ helper functions++-- | extract the main state for each node (eg MP state for MATP node)++-- TODO shouldn't this just be "head $ nstates n"?++nodeMainState :: CM n s -> Node n -> State s+nodeMainState cm n = head $ filter ((==st) . stype) ss where+  (Just st) = (ntype n) `lookup` nodeMainStateAssocs+  ss = map (states cm !) $ nstates n+++-- | Checks for each node, if it can be target of a local begin.++localBeginPossible :: CM n s -> Node n -> Bool+localBeginPossible cm n =+  if ntype n `elem` okNodes+  && (not . any (==0) $ nparents n) -- nodes reachable from "root" (that is: node 1) have handled specially+    then True+    else False+  where+    okNodes = [MATP,MATL,MATR,BIF]++++-- | Checks for each node if it can lead to a local end.++localEndPossible :: CM n s -> Node n -> Bool+localEndPossible cm n =+  if ntype n `elem` okNodes+  && (END /= (ntype $ nodes cm ! (nid n +1)))+    then True+    else False+  where+    okNodes = [MATP,MATL,MATR,BEGL,BEGR]++++-- | transform scores into probabilities, given a nullmodel for x++-- TODO quickcheck!++score2Prob x null+  | x == (-1/0) = 0+  | otherwise   = exp (x * log 2) * null++++-- | back into scores++prob2Score x null+  | x == 0    = (-1/0)+  | otherwise = log (x / null) / log 2++++-- | Transform a state, setting probabilities instead of scores. Requires CM+-- knowledge for background model.++-- TODO actually use the background model++stateScore2Prob :: CM n s -> State s -> State s+stateScore2Prob cm s = error "implement me"++++-- | Transform a state, setting scores instead of probabilities.++stateProb2Score :: CM n s -> State s -> State s+stateProb2Score cm s = error "implement me"+transitionTargets :: [Transition] -> [Int]+transitionTargets xs = map f xs where+  f (Branch x)       = x+  f (Transition x _) = x+++nodeMainStateAssocs :: [(NodeType,StateType)]+nodeMainStateAssocs =+  [ (MATP, MP)+  , (MATL, ML)+  , (MATR, MR)+  , (BIF,  B)+  , (ROOT, S)+  , (BEGL, S)+  , (BEGR, S)+  , (END,  E)+  ]++-- }}}++++-- TODO score -> prob : exp (x / log 2) -- CHECK THIS!!!+-- score -> prob : exp (x * log 2)+-- prob -> score : (log x) / log 2+-- TODO mkGlobal (needed?)+-- TODO use logsum : log (exp x + exp y) = x + log (1 + exp (y-x)), where x>y

@@ -0,0 +1,76 @@+{-# LANGUAGE RecordWildCards #-}++-- | write an Infernal model. We aim for version 1.0.2 of Infernal but right+-- now, there is no explicit version management! We just return header+-- information as we read it. So we are compatible to all versions that can be+-- parsed but have no safeguards in place.+--+-- NOTE: exported model can apparently be calibrated.+--+-- TODO make sure that (Export.toString . Import.fromString == id); the other+-- way around is not absolutely necessary (except if the Infernal parser should+-- require this at some point)+--+-- TODO put functions like stringS into another module?++module Biobase.Infernal.CM.Export where++import qualified Data.Array.IArray as A+import Text.Printf++import Biobase.Infernal.CM++import Biobase.Infernal.CM.Import -- TODO for testing only!++++-- | Main export function for CMs. Creates a string that is accepted by+-- Infernal++toString :: CM n s -> String+toString cm@CM{..} = unlines $ hdr ++ ["MODEL:"] ++ nds ++ ["//"]+  where+    hdr = map (\(k,v) -> k ++ " " ++ v) header+    nds = concatMap (nodeToString cm) $ A.elems nodes++++-- | export a specific node, used by 'toString'++nodeToString :: CM n s -> Node n -> [String]+nodeToString cm Node{..} = printf "\t\t\t\t[ %s %d ]" (show ntype) nid : map (stateToString cm . (states cm A.!)) nstates++++-- | export a specific states, used by 'nodeToString'++stateToString :: CM n s -> State s -> String+stateToString cm State{..} = printf "    %2s %6d %6d %2d %6d %6d %-55s %s" (show stype) sid maxP numP minC numC tscores escores+  where+    maxP+      | null sparents = -1+      | otherwise     = maximum sparents+    numP = length sparents+    minC+      | null schildren = -1+      | otherwise      = minimum $ map tchild schildren+    numC+      | stype == B = maximum $ map tchild schildren+      | otherwise  = length schildren+    tscores :: String+    tscores+      | stype == B = ""+      | otherwise  = concatMap (printf "%s   " . stringS . tscore) schildren+    escores :: String+    escores+      | null semission = ""+      | otherwise      = concatMap (printf "%.3f " . escore) semission++++-- | export scores for transitions with the Infernal-specific "-infinity" value+-- of "*"++stringS x+  | x == (-1/0) = "      *"+  | otherwise   = printf "%.3f" x

@@ -0,0 +1,194 @@++--+-- A parser for Infernal's Covariance Models (CM). Should work with version 1.0+-- of Infernal.+--++-- TODO use generics?+--+-- TODO importing the cmcalibrate calibration data is currently broken! (data is parsed as separate lines)++module Biobase.Infernal.CM.Import (fromFile,fromString) where++import Data.Maybe (fromJust)+import qualified Data.Array.IArray as A+import qualified Data.List as L+import Text.ParserCombinators.Parsec hiding (State)++import Biobase.Infernal.CM+import Biobase.RNA hiding (nucE)++++-- {{{ Parsec++myChar = alphaNum <|> char '-' <|> char '_' <|> char '.'+headerChar = myChar <|> char '[' <|> char ']'+floating = many1 $ digit <|> char '.' <|> char 'e' <|> char '-'++headerLine = do+  key <- many1 headerChar+  --spaces+  many1 $ char ' '+  val <- many1 (headerChar <|> char ' ' <|> char '/' <|> char ':')+  newline+  return (key,val)++unknownNumbers = do+  many1 $ char ' '+  ns <- floating `sepEndBy` (many1 $ char ' ')+  newline+  return ("",concat ns)++theHeader = do+  hs <- many $ (try headerLine <|> try unknownNumbers)+  string "MODEL:"+  newline+  return hs++-- }}}++-- {{{ Node++node = do+  spaces+  string "[ "+  name <- many letter+  spaces+  num <- many digit >>= (return . read)+  spaces+  string "]"+  newline+  states <- many $ try (state num)+  return $ (Node+             { ntype = read name+             , nid = num+             , nstates = map sid states+             , nparents = []+             , nchildren = []+             , ntag = ()+             }+            , states)++-- }}}++-- {{{ stuff++-- TODO put some of this into HsTools/Parsec stuff++aNum = many1 $ char '-' <|> digit+addneginf :: String -> Double+addneginf "*" = (-1)/0 --"-1000000000.0"+addneginf x = read x++-- }}}++-- {{{ State++state nodeID = do+  spaces+  name <- many1 myChar+  spaces+  sid <- aNum >>= (return . read)+  spaces+  plast <- aNum >>= (return . read)+  spaces+  pnum <- aNum >>= (return . read)+  spaces+  cfirst <- aNum >>= (return . read)+  spaces+  cnum <- aNum >>= (return . read)+  probs <- ( (many $ myChar <|> char '*') `sepBy` (many1 $ char ' ') >>=+             return . map addneginf . filter ((/=) "") )+  newline+  let s = case name of+            "B" -> State+                    { stype = read name+                    , sid = sid+                    , snode = nodeID+                    , sparents = [plast-pnum+1 .. plast]+                    , schildren = [Branch cfirst, Branch cnum]+                    , semission = []+                    , stag = ()+                    }+            _   -> State+                    { stype = read name+                    , sid = sid+                    , snode = nodeID+                    , sparents = [plast-pnum+1 .. plast]+                    , schildren = zipWith Transition [cfirst .. cfirst+cnum-1] probs+                    , semission = let keep = drop cnum probs in+                        case length keep of+                          0  -> []+                          4  -> zipWith EmitS acgu keep+                          16 -> zipWith (\(k1,k2) v -> EmitP k1 k2 v) acguPairs keep+                          _  -> error $ "strange number of probabilities" ++ show (keep)+                    , stag = ()+                    }+  return s++-- }}}++-- {{{ Model++models = do+  ms <- many model+  eof+  return ms++model = do+  h <- theHeader+  ns <- many node+  let states = concatMap snd ns+  let nodes = map (addPCinfo states . fst) ns+  -- just add all the node parent / child info+  string "//"+  newline+  -- eof -- removed, we want to be able to read concatenated models!+  return $ CM+            { nodes      = A.array (0, length nodes -1)  $ zip (map nid nodes)  nodes+            , states     = A.array (0, length states -1) $ zip (map sid states) states+            , header     = h+            , localBegin = A.array (0, length states -1) $ zip [0 .. length states -1] (0.0 : repeat (-1/0))+            , localEnd   = A.array (0, length states -1) $ zip [0 .. length states -1] (repeat (-1/0))+            , cmType     = CMScore+            , nullModel  = A.array (nucA,nucU) $ zip acgu (map read . words . fromJust $ "NULL" `lookup` h) -- TODO circumvents the whole parsing stuff!+            }++-- }}}++-- {{{ Stuff++addPCinfo states n =+  let+    s = nstates n+    sp = L.nub $ L.sort $ concatMap (sparents . (states !!)) s+    sc = L.nub $ L.sort $ concatMap (transitionTargets . schildren . (states !!)) s+    np = (L.nub $ L.sort $ map (snode . (states !!)) sp) L.\\ [nid n]+    nc = (L.nub $ L.sort $ map (snode . (states !!)) sc) L.\\ [nid n]+  in+    n {nparents = np, nchildren = nc}++++-- | Two types of parsing, once using a file and once by parsing a string.++fromFile f = parseFromFile models f+fromString s = parse models "(stdin)" s++-- }}}++-- | Helper function to remove impossible state transitions (those that have+-- -infty score).++-- TODO move to InfernalCM.hs and have it for Prob and Score both++{-+canonize cm = cm {states = A.amap f $ states cm} where+  f s = s {schildren = filter g $ schildren s}+  g (Branch _)    = True+  g (Transition _ v) = +  h (_,s)+    | s == (-1)/0 = False+    | otherwise   = True+-}

@@ -0,0 +1,16 @@++-- | The beginnings of a Stockholm File parser.++module Biobase.Infernal.Stockholm where++-- | Stockholm format data. We have a set of sequences with sequence data, a+-- set of column annotations and unknown data (actually: known, but we do not+-- care).++data Stockholm = Stockholm+  { sequences :: [(String,String)]+  , colAnnotations :: [(String,String)]   -- #=GC tag+  , exAnnotations :: [(String,String)]    -- NOTE this is not in the Stockholm format!+  , unknown :: [String]+  }+  deriving (Show)

@@ -0,0 +1,35 @@++-- | A simple parser for Stockholm data. As we do not interpret most stuff+-- right now, Parsec is not required.++module Biobase.Infernal.Stockholm.Import where++import Biobase.Infernal.Stockholm+import Data.List++fromFile :: String -> IO Stockholm+fromFile fname = do+  ls <- readFile fname >>= return . filter (not . null) . lines+  let (colanno, rest1) = partition (\x -> length x >= 4 && (and $ zipWith (==) "#=GC" x)) ls+  let (seqdata, rest2) = partition (\(x:_) -> x/='#' && x/='/') rest1+  let (exdata , unk)   = partition (\x -> length x >= 4 && (and $ zipWith (==) "#=EX" x)) rest2+  {-+  print colanno+  print rest1+  print seqdata+  print rest2+  print exdata+  print unk+  -}+  return Stockholm+    { sequences      = map (mkPair . words) seqdata+    , colAnnotations = map (mkPair . drop 1 . words) colanno+    , exAnnotations  = map (mkPair . drop 1 . words) exdata+    , unknown        = unk+    }++++mkPair []     = error "empty list"+mkPair [x]    = error $ "just one element: " ++ show x+mkPair (x:xs) = (x,unwords xs)

@@ -0,0 +1,36 @@+name:           BiobaseInfernal+version:        0.0.2.0+author:         Christian Hoener zu Siederdissen+maintainer:     choener@tbi.univie.ac.at+category:       Bioinformatics+synopsis:       Infernal CM manipulation+license:        GPL-3+license-file:   LICENSE+build-type:     Simple+stability:      experimental+cabal-version:  >= 1.4.0+description:+                This library provides functions to load Infernal covariance+                models. Models can be converted from score mode into+                probability mode. They, too, can be switched into local mode.+                In additon, Stockholm files can be loaded.+++library+  build-depends:+    base >= 4 && < 5,+    parsec >= 3 && < 4,+    containers,+    array,++    Biobase >= 0.0.2 && < 0.0.3++  exposed-modules:+    Biobase.Infernal.CM+    Biobase.Infernal.CM.Import+    Biobase.Infernal.CM.Export+    Biobase.Infernal.Stockholm+    Biobase.Infernal.Stockholm.Import++  ghc-options:+    -O2

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@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain