diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,340 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Library General Public License instead.) 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Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. 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 Library General +Public License instead of this License. diff --git a/README b/README new file mode 100644 --- /dev/null +++ b/README @@ -0,0 +1,39 @@ +This contains the following tools: + +To build these, you will need a Haskell compiler (the most likely +candidate begin GHC), and my bioinformatics library and the SimpleArgs +module installed (Downloadable from: ). + +filter - remove unwanted sequences from a clustering + usage: filter seq.list < cluster.L > cluster2.L + cluster2.L will only contain sequence labels found in seq.list + +hist - produce a histogram of cluster sizes from a "label"-formatted + clustering. + +clusc - compare clusterings, calculating numerous pair-based and + entropy based indices. + +xcerpt - given a file containing a list of sequence labels (e.g. a + "label" formatted clustering), extract matching sequences + from a FASTA file. Like "agrep -d '^>'" without the bugs. + + Usage: xcerpt list.txt fasta.seq + creates "fasta.seq.match" and "fasta.seq.rest" + +add_single - add singletons to a clustering. + Usage: add_single all.L clustering.L + creates clustering.L_s listing all sequences in all.L but not in + clustering.L, one per line. + +ace2contigs - parse an ACE assembly file, and output the contigs in a + FASTA file (named by tacking on .fasta to the ACE file name), + and the corresponding quality information (.qual). + +ace2fasta - parse an ACE assembly, and output each assembly in a separate + fasta formatted file, with the necessary gaps inserted to align the + sequences (suitable for import into e.g. Seaview) + +clusterlibs - given a table of regular expressions and library names, + along with a clustering (TGICL-format), output a table of clusters + with the library name prepended to the sequences. diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,3 @@ +#!/usr/bin/env runhaskell +import Distribution.Simple +main = defaultMain diff --git a/clustertools.cabal b/clustertools.cabal new file mode 100644 --- /dev/null +++ b/clustertools.cabal @@ -0,0 +1,65 @@ +Name: clustertools +Version: 0.1 +License: GPL +License-file: LICENSE +Author: Ketil Malde +Maintainer: Ketil Malde + +Category: Bioinformatics +Synopsis: Tools for manipulating sequence clusters +Description: This is a bunch of stuff I needed at some for manipulating sequence + clusters. See the README for details. The tools included are: + . + * filter - remove unwanted sequences from a clustering + . + * hist - produce a histogram of cluster sizes from a "label"-formatted clustering. + . + * clusc - compare clusterings, calculating numerous pair-based and entropy based indices. + . + * add_single - add singletons to a clustering. + . + * ace2contigs - parse an ACE assembly file, and output the contigs in a FASTA file. + . + * ace2fasta - parse an ACE assembly, and output each assembly in a separate FASTA file + . + * clusterlibs - given a table of regular expressions and library names, along with a + clustering (TGICL-format), output a table of clusters with the library name + prepended to the sequences. + . + The Darcs repository is at: . +Homepage: http://malde.org/~ketil/ + +Tested-With: GHC==6.8.2 +Build-Type: Simple +Cabal-Version: >= 1.2 + +Data-Files: README + +Executable filter + Hs-source-dirs: src + Main-Is: Filter.hs + Build-Depends: base>3, containers, simpleargs>=0.1 + ghc-options: -Wall -O2 -funbox-strict-fields + +Executable clusc + Hs-source-dirs: src + Main-Is: Cluscomp.lhs + Build-Depends: bytestring + +Executable add_single + Hs-source-dirs: src + Main-Is: AddSingletons.hs + +Executable ace2contigs + Hs-source-dirs: src + Main-Is: Ace2Contigs.hs + Build-depends: bio>=0.3.3 + +Executable ace2fasta + Hs-source-dirs: src + Main-Is: Ace2Fasta.hs + +Executable clusterlibs + Hs-source-dirs: src + Main-Is: ClusterLibs.hs + Build-depends: regex-compat diff --git a/src/Ace2Contigs.hs b/src/Ace2Contigs.hs new file mode 100644 --- /dev/null +++ b/src/Ace2Contigs.hs @@ -0,0 +1,17 @@ +-- ace2contigs +-- Extract the contigs with quality information from ace file + +module Main where +import Prelude hiding (reads) + +import Bio.Alignment.ACE +import Bio.Sequence + +import System.SimpleArgs (getArgs) + +main :: IO () +main = do + ace <- getArgs + a <- readACE ace + let cs = map (fst . contig) $ concat a + writeFastaQual (ace++".fasta") (ace++".qual") cs diff --git a/src/Ace2Fasta.hs b/src/Ace2Fasta.hs new file mode 100644 --- /dev/null +++ b/src/Ace2Fasta.hs @@ -0,0 +1,29 @@ +-- ace2fa +-- Read an ACE file, output in Fasta format +-- (for importing into seaview) + +module Main where +import Prelude hiding (reads) + +import Bio.Alignment.ACE +import Bio.Sequence +import qualified Data.ByteString.Lazy.Char8 as B +import System.SimpleArgs (getArgs) +import System.IO + +main :: IO () +main = do + a <- readACE =<< getArgs + mapM_ (\ss -> writeFasta (B.unpack $ seqlabel $ head ss) ss) (map pad_all $ concat a) + +pad_all :: Assembly -> [Sequence] +pad_all asm = pad 21 (contig asm) : map padRead (reads asm) + where padRead (off,_dir,sq,gs) = pad (20+off) (sq,gs) -- note: they are already complemented + +-- generate a sequence with '-' for gaps +pad :: Offset -> (Sequence,Gaps) -> Sequence +pad off (Seq n s _,gs) = let s' = (if off < 0 then B.drop (negate off) else B.append (B.replicate off '-')) (insertGaps '-' (s,gs)) + in (Seq n s' Nothing) + + + diff --git a/src/AddSingletons.hs b/src/AddSingletons.hs new file mode 100644 --- /dev/null +++ b/src/AddSingletons.hs @@ -0,0 +1,30 @@ +-- add singleton clusters to clustering files +-- read files building map over words +-- add the difference + +-- usage: add_single reference clustering1 [clustering2].. + +import System.Environment (getArgs) +import System.IO +import Control.Monad +import Data.Set + +main = do + (ref:fs) <- getArgs + r <- readFile ref + mapM_ (append_s (mkindex r)) fs + +append_s :: Set String -> FilePath -> IO () +append_s ref f = do + fc <- readFile f + let fi = mkindex fc + when (not . Data.Set.null . difference fi $ ref) + (putStrLn ("Warning: '"++f++"' contains unknown words!")) + let ss = difference ref fi + when (Data.Set.null ss) (return ()) + h <- openFile (f++"_s") WriteMode + mapM_ (hPutStrLn h) (toList ss) + hClose h + +mkindex :: String -> Set String +mkindex = foldr insert empty . words diff --git a/src/Cluscomp.lhs b/src/Cluscomp.lhs new file mode 100644 --- /dev/null +++ b/src/Cluscomp.lhs @@ -0,0 +1,175 @@ + +Calculate the contingency matrix for two clusterings. +For clusterings $C = {c_1,c_2,...c_n} and $K = {k_1, k_2,..k_m}$ +the matrix is defined as $ a_ij = c_i U k_j $. + +The matrix is calculated lazily, and arbitrary functions can +be applied to it to derive various scores: edit distance, +jaccard index, exact count, etc. + +\begin{code} + +module Main where + +import qualified Data.ByteString.Lazy.Char8 as B + +import Data.Map hiding (map,filter,null) +import qualified Data.Map as M +import Data.List +import Data.Maybe +import System.Environment (getArgs) +import Text.Printf + +type ByteString = B.ByteString + +main :: IO () +main = do + (a:args) <- getArgs + a' <- B.readFile a + let ref = mkC $ readC a' + n = maximum $ map length ("clustering":args) + putStrLn (pad n "clustering" ++ "\tVI\tMIF\tJaccard\tRand\tFowMal\tSkew") + mapM_ (comp n ref) args + +pad i s = s ++ replicate (i-length s) ' ' + +comp :: Int -> Clustering -> FilePath -> IO () +comp n k f = do + f' <- B.readFile f + let mx = matrix k (readC f') + ct = mkPairs k mx + sh = printf "%.3f" + putStrLn $ concat $ intersperse "\t" $ (pad n f) : map sh + [fst $ iscore mx -- VI + ,snd $ iscore mx -- MIF + ,jaccard ct, rand ct, fowmal ct, skew ct] -- ++"\tmatrix: "++show ct) + +type CID = Int + +type Sequence = ByteString -- hash for efficiency? +type Cluster = [Sequence] + +type Clustering = (Map CID Cluster + ,Map Sequence CID) -- optimization option + +cid :: Clustering -> Sequence -> Maybe CID +cid k x = M.lookup x (snd k) + +seqs :: Clustering -> CID -> Maybe Cluster +seqs k c = M.lookup c (fst k) + +-- read a clustering from file +readC :: ByteString -> [Cluster] +readC = filter (not.null) . map B.words . B.lines + +-- build the Clustering from a set of clusters +mkC :: [Cluster] -> Clustering +mkC = foldr ins (M.empty,M.empty) . zip [0..] + where ins (n,ss) (i2c,s2i) = (M.insert n ss i2c, foldr (\s -> M.insert s n) s2i ss) + +\end{code} + +Matrix construction. + +\begin{code} + +type Row = [(Maybe CID,[Sequence])] +type Matrix = [Row] + +-- reads a clustering and produces the confusion (-tingency) matrix +matrix :: Clustering -> [[Sequence]] -> Matrix +matrix c = map (matrixRow c) + +matrixRow :: Clustering -> [Sequence] -> Row +matrixRow k c1 = comb $ sort $ map (\x -> (cid k x, [x])) c1 -- cid,seq + where comb ((a,b):(c,d):xs) | a==c = comb ((a,b++d):xs) + | otherwise = (a,b):comb ((c,d):xs) + comb [(a,b)] = [(a,b)] + comb [] = [] + +\end{code} + +\subsection{Jaccard index, and friends} + +Indices based on pair counts. This includes jaccard, rand, ...? +"skew" is based on MacNemar's test. + +\begin{code} + +type Pairs = (Double,Double,Double,Double) -- a b c, and d + +jaccard, rand, fowmal, skew :: Pairs -> Double +jaccard (a,b,c,_) = a/(a+b+c) +rand (a,b,c,d) = (a+d)/(a+b+c+d) +fowmal (a,b,c,d) = a/sqrt((a+b)*(a+c)) -- Fowlkes-Mallows index +-- this is the same as fowmal (why?)! +hubert (a,b,c,d) = (a*d - b*c)/sqrt((a+b)*(c+d)*(a+c)*(b+d)) -- Gamma stat? + +skew (a,b,c,d) = (b-c)/sqrt(b+c)/sqrt d + +mkPairs :: Clustering -> Matrix -> Pairs +mkPairs k m = let (a,b,c,ct) = foldl (jc1 k) (0,0,0,0) m + in (a/2,b/2,c/2,(ct*(ct-1)-a-b-c)/2) + +-- this is pretty ugly! +jc1 :: Clustering -> Pairs -> Row -> Pairs +jc1 k j row = let row' = filter (isJust.fst) row + l = sum $ map (len.snd) row' + in foldr (jc2 k l) j row' +jc2 k lc (Just i,ss) (a,b,c,ct) = (a+ls*(ls-1),b+(ls*(lk-ls)),c+(ls*(lc-ls)),ct+ls) + where ls = len ss + lk = len $ fromJust (seqs k i) -- fixme! only seqs found in C! + +-- todo: accumulate column sizes until end? how does clusqual deal? + +\end{code} + +\subsection{Entropy-based measures} + +The \texttt{iscore} function calculates the variation of information +between the two clustrings. Given clusterings $C$ and $K$ matrix $H$, it is +calculated as: + +\( + \sum_C H_c\log H_c + \sum_K H_k\log H_k -2\sumH_{K,C} H_{k,c} \log H_{k,c} +\) + +Todo: implement \[I/H = (H_c - H_k)/H_{c,k} - 1\] + +I.e. collect H_k, H_c,k, and H_c, and use it to calculate both measures. + +\begin{code} + +type Imx = (Double,Double,Double,Double) + +-- iscore calculates mutual information fraction and variation of information +iscore :: Matrix -> (Double,Double) -- MIF and VI +iscore mx = let (n,hc,hk,hck) = iscores empty (0,0,0,0) mx + vi = 1/n*(-2*hck+hc+hk) + mif = (hc+hk-2*mlog n)/(hck-mlog n)-1 + in (vi,mif) + +-- iscores - calculate n, H_c, H_k, H_c,k +iscores:: Map Int Double -> Imx -> Matrix -> Imx +iscores m (n,hc,hk,hck) (r:rs) = + let r' = map (len.snd) $ filter (isJust.fst) r + in iscores (accum m r) + (n+sum r',hc,hk+mlog (sum r'),hck+sum (map mlog r')) rs +iscores m (n,hc,hk,hck) [] = + (n,(sum $ map mlog $ elems m),hk,hck) + +-- accumulate the column sums for the matrix. This must be done +-- explicitly, since one clustering may contain sequences not present +-- in the other +accum :: Map Int Double -> Row -> Map Int Double +accum m row = foldr accum1 m row + where accum1 (Just cid,seqs) m = insertWith (+) cid (len seqs) m + accum1 (Nothing,_) m = m + +mlog 0 = 0 -- error "log 0!" +mlog x = x*log x/log 2 + +len = fromIntegral . length + +\end{code} + diff --git a/src/ClusterLibs.hs b/src/ClusterLibs.hs new file mode 100644 --- /dev/null +++ b/src/ClusterLibs.hs @@ -0,0 +1,66 @@ +-- clusterLibs +-- calculate clusters by library, using the lib table +-- read patterns from a table, first line is header + +{- +import qualified Data.ByteString.Char8.Lazy as B +import Data.Map (Map) +import qualified Data.Map as M + + +type Str = B.ByteString +type Clusters = Map Str [Str] + +insert1 m k v = M.insertWith (flip (++)) k [v] m +-} + +import System.Environment (getArgs) +import Text.Regex +import Data.List (elemIndex,sortBy,intersperse) + +type Cluster = (String,[String]) + +main = do + [ps,cs] <- getArgs `catch` error "Usage: clusterlibs ps cs" + pat <- readPatternTable ps + clus <- classClusters pat cs + writeClusters clus + +readPatternTable :: FilePath -> IO [(Regex,String)] +readPatternTable f = do + (h:ls) <- return . map words . lines =<< readFile f + let (p,n) = case (elemIndex "Pattern" h, elemIndex "Name" h) of + (Just x,Just y) -> (x,y) + _ -> error ("Need both 'Pattern' and 'Name' headers in '"++f++"'") + z l = (mkRegex (l!!p),l!!n) + return $ map z ls + +-- will need to match against all, to check for multiple matches +-- tag names with library +classClusters :: [(Regex,String)] -> FilePath -> IO [Cluster] +classClusters ps f = return . getClusters (classify ps) . lines =<< readFile f + +classify ps str = case concatMap (class1 str) ps of + [] -> error ("no match for "++str) + [x] -> x++":"++str + s@(_:_) -> error ("multiple matches for "++str++": "++show s) + where class1 str (r,s) = maybe [] (const [s]) (matchRegex r str) + +getClusters f [] = [] +getClusters f [_] = error "odd number of cluster lines!" +getClusters f (c:ss:rest) = case head $ words c of + ('>':name) -> (name,map f $ words ss) : getClusters f rest + _ -> error ("Cluster '"++c++"' didn't start with '>'") + +-- transpose and print +writeClusters :: [Cluster] -> IO () +writeClusters cs = do + let cs' = map (\(h,s) -> (h:s)) cs + cs'' = sortBy (\x y -> compare (length y) (length x)) cs' + unwords' = concat . intersperse "," + putStrLn $ unlines $ map unwords' $ transpose cs'' + +transpose :: [[String]] -> [[String]] +transpose [] = [] +transpose ls' = let ls = filter (not . null) ls' + in map head ls : transpose (map tail ls) diff --git a/src/Filter.hs b/src/Filter.hs new file mode 100644 --- /dev/null +++ b/src/Filter.hs @@ -0,0 +1,10 @@ + +import System.SimpleArgs +import Data.Set hiding (filter,map,null) + +main :: IO () +main = interact . runFilter . fromList . words =<< readFile =<< getArgs + +runFilter :: Set String -> String -> String +runFilter s = unlines . filter (not.null) . + map (unwords . filter (flip member s) . words) . lines