bioace (empty) → 0.0
raw patch · 4 files changed
+993/−0 lines, 4 filesdep +basedep +bioaligndep +biocoresetup-changed
Dependencies added: base, bioalign, biocore, bytestring, haskell98, parsec
Files
- LICENSE +701/−0
- Setup.hs +2/−0
- bioace.cabal +23/−0
- src/Bio/Alignment/Ace.hs +267/−0
+ LICENSE view
@@ -0,0 +1,701 @@+ GNU GENERAL PUBLIC LICENSE+ Version 3, 29 June 2007++ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>+ 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. By contrast,+the GNU General Public License is intended to guarantee your freedom to+share and change all versions of a program--to make sure it remains free+software for all its users. We, the Free Software Foundation, use the+GNU General Public License for most of our software; it applies also to+any other work released this way by its authors. You can apply it to+your programs, too.++ When we speak of free software, we are referring to freedom, not+price. 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+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ bioace.cabal view
@@ -0,0 +1,23 @@+Name: bioace+Version: 0.0+Description: Library for reading ace assembly files+Synopsis: Library for reading ace assembly files+Homepage: https://patch-tag.com/r/dfornika/bioace/home+License: GPL+License-file: LICENSE+Cabal-Version: >=1.6+Author: Dan Fornika <dfornika@gmail.com>+Maintainer: dfornika@gmail.com+Stability: Provisional+Category: Bioinformatics+Build-Type: Simple++Library+ Build-depends: base >= 2 && < 5, haskell98, biocore, bioalign, bytestring, parsec+ Exposed-modules: Bio.Alignment.Ace+ Hs-source-dirs: src++source-Repository head+ type: darcs+ location: http://www.patch-tag.com/r/dfornika/bioace+
+ src/Bio/Alignment/Ace.hs view
@@ -0,0 +1,267 @@+{- |+ Read ACE format assembly files++ These are typically output by sequence assembly tools,+ like CAP3 or Phrap.++ Documented in the section labelled \"ACE FILE FORMAT\" at+ <http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt>++ Briefly: each field is a line starting with a two letter code,+ in some cases followed by data lines termintated by a blank line.+ Here's an brief example how an ACE file looks like:++ @+ AS contigs reads+ CO contig_name bases reads segments compl (CAP3: segments=0)+ sequence+ BQ base_qualities+ AF read1 compl padded_start_consensus (negatives meaning?)+ AF read2 ..+ BS segments+ RD read1 bases info_items info_tags (latter two set to 0 by CAP3)+ sequence+ QA read1 qual_start qual_end align_start align_end+ DS (phred header? left empty by CAP3)+ RD read2 ...+ @++ As far as I know, this is only used for nucleotide sequences.+-}++{-# LANGUAGE CPP #-}++module Bio.Alignment.Ace (readACE, writeACE, Assembly(..), ptest, reads ) where++import Prelude hiding (lines,words,readFile,unwords -- ByteString clashes+ ,reads,pred -- Assembly clash+ )++import Bio.Core.Sequence+import Bio.Core.Strand+import Bio.Alignment.AlignData (Sequence(..), Gaps, Alignment, extractGaps)++import qualified Data.ByteString.Lazy.Char8 as B+import Data.ByteString.Lazy.Char8 (ByteString,words,pack,unpack,readFile,unwords)++import Text.ParserCombinators.Parsec+import Text.ParserCombinators.Parsec.Pos (newPos)++import Control.Monad (liftM) -- ,when?+import Data.Char (chr)++instance Show Sequence where+ show (Seq lab seq qual) = unpack $ unSD seq++data Assembly = Asm { contig :: (Sequence, Gaps), fragments :: Alignment}+ deriving Show++{-# DEPRECATED reads "Stupid name, replaced by 'fragments'." #-}+reads :: Assembly -> Alignment+reads = fragments -- deprecated, stupid, stupid name.++type Str = ByteString++-- | ACE header lines with parameters+-- The tokenizer (scanner) should convert input into a list of these,+-- which in turn can be parsed by Parsec+data ACE = AS Str Str | CO Str Str Str Str Str+ | BQ | AF Str Str Str | BS [Str]+ | RD Str Str Str Str+ | QA Str Str Str Str Str+ | DS [Str] | Other [Str] | Empty+ deriving (Eq)++instance Show ACE where+ show (AS x y) = "AS "++uw [x,y]+ show (CO a b c d e) = "CO "++uw [a,b,c,d,e]+ show BQ = "BQ"+ show (AF a b c) = "AF "++uw [a,b,c]+ show (RD a b c d) = "RD "++uw [a,b,c,d]+ show (QA a b c d e) = "QA "++uw [a,b,c,d,e]+ show (DS ss) = "DS "++uw ss+ show (Other ss) = uw ss+ show Empty = "(blank)"+ show _ = "unknown ACE string"++uw :: [Str] -> String+uw = unpack . unwords++-- | The Parsec parser type+type AceParser a = GenParser (SourcePos,ACE) () a++-- | Parse a single token, primitive parser+parse1 :: (ACE -> Maybe a) -> AceParser a+parse1 p = token sho pos pred+ where sho (_,t) = show t+ pos (n,_) = n+ pred (_,t) = p t++-- | Test parser p on a list of ACE elements+ptest :: Show a => String -> AceParser a -> [ACE] -> IO ()+ptest m p = parseTest p . source m++-- | Add SourcePoses to a stream of ACEs.+source :: String -> [ACE] -> [(SourcePos,ACE)]+source m = zip (iterate (\sp -> incSourceLine sp 1) (newPos m 1 0))++-- | Parse a complete ACE file as a set of assemblies.+ace :: AceParser [[Assembly]]+ace = many1 ace1++ace1 :: AceParser [Assembly]+ace1 = do+ as+ many blank+ many (do ctg >>= asm) -- apparently, CAP3 outputs empty assemblies (AS 0 0)++-- | parse the initial header+as :: AceParser (Int,Int)+as = parse1 (\t -> case t of AS cs rs -> do c <- B.readInt cs+ r <- B.readInt rs+ return (fst c,fst r)+ _ -> Nothing) <?> "AS <int> <int>"++blank :: AceParser ()+blank = parse1 (\t -> case t of Empty -> Just ()+ _ -> Nothing) <?> "empty line"++-- | parse the contig and quality information (CO, BQ)+ctg :: AceParser (Sequence, Gaps)+ctg = do+ name <- co+ sd <- sdata+ let (sd',gaps) = extractGaps $ SeqData {unSD = sd}+ many blank+ -- Vector NTI produces ACE without BQ for the contig+ msq <- do bq+ sq <- qdata+ return (Just $ QualData {unQD = sq})+ <|> return Nothing+ many blank+ -- todo: gaps?+ return (Seq (SeqLabel {unSL = name}) sd' msq, gaps)++co, sdata, qdata :: AceParser Str+co = parse1 (\t -> case t of CO name a b c _compl -> do+ _bs <- B.readInt a+ _rds <- B.readInt b+ _seg <- B.readInt c+ return name+ _ -> Nothing) <?> "CO name <int> <int> <int> bool"++sdata = do return . B.concat =<< many1 sdata1+ where sdata1 = parse1 (\t -> case t of Other sd -> Just (unwords sd)+ _ -> Nothing) <?> "sequence data"++qdata = do return . B.concat =<< many1 qdata1+ where qdata1 = parse1 (\t -> case t of Other sd -> liftM (pack . map chr) (readInts sd)+ _ -> Nothing) <?> "sequence data"++-- | Read a list of Ints in the Maybe monad+readInts :: [ByteString] -> Maybe [Int]+readInts [] = Just []+readInts (x:xs) = do (i,_) <- B.readInt x+ is <- readInts xs+ return $ (i:is)++bq :: AceParser ()+bq = parse1 (\t -> case t of BQ -> Just (); _ -> Nothing) <?> "BQ"++-- | Given the CO info, get the AFS'es+asm :: (Sequence, Gaps) -> AceParser Assembly+asm cg = do+ many blank+ afs <- many1 af+ _bss <- many bs+ many blank+ rds cg afs++-- | Parse a list of AFS, followed by actual read, and merge them+-- afs :: Sequence -> AceParser [Sequence] -- plus some auxiliary info?+af :: AceParser (Str, Strand, Offset)+af = parse1 (\t -> case t of AF a b c -> mkAF a b c+ _ -> Nothing) <?> "AF name (U|C) pad_start"+ where mkAF a b c = do+ b' <- case unpack b of "U" -> Just Plus; "C" -> Just Minus; _ -> Nothing+ c' <- liftM (fromIntegral . fst) (B.readInt c)+ return (a,b',c')++bs :: AceParser (Int,Int,Str)+bs = parse1 (\t -> case t of BS [x,y,n] -> do + x' <- readInt' x+ y' <- readInt' y+ return (x',y',n)+ _ -> Nothing) <?> "BS x y name"++readInt' :: Str -> Maybe Int+readInt' = liftM (fromIntegral . fst) . B.readInt++rds :: (Sequence,Gaps) -> [(Str, Strand, Offset)] -> AceParser Assembly+rds cg xs = do+ r <- many1 rseq+ -- todo: check the number and merge with the afs+ let f (_name,d,off) (s,gs) = (off,d,s,gs)+ return $ Asm { contig = cg, fragments = zipWith f xs r }++rseq :: AceParser (Sequence, Gaps)+rseq = do+ (rn,_len,_,_) <- rd+ (s,gaps) <- return . (\x -> extractGaps $ SeqData {unSD = x}) =<< sdata+ -- when (B.length s == fromIntegral len) $ (fail "Incorrect sequence length!")+ -- todo: fix gaps!+ many1 blank+ qa+ ds+ many blank+ return (Seq (SeqLabel {unSL = rn}) s Nothing,gaps) -- huh?++-- | parse each read (RD, QA, DS)+-- Vector NTI appears to insert solitary RDs, sometimes even without any sequence data!?+-- This is not supported at this point.+rd :: AceParser (Str,Int,Int,Int)+rd = parse1 (\t -> case t of RD a b c d -> do [x,y,z] <- readInts [b,c,d]+ return (a,x,y,z)+ _ -> Nothing) <?> "RD <string> <int> <int> <int>"++qa :: AceParser ()+qa = parse1 (\_ -> Just ())++ds :: AceParser ()+ds = parse1 (\t -> case t of DS _ -> Just (); _ -> Nothing) <?> "DS"++-- ----------------------------------------------------------+-- Convert lines into tokens+tokenize :: ByteString -> [ACE]+tokenize = map tokenize1 . B.lines++-- Tokenise a single line+-- todo: error on incorrect (partial) format, error reports with line number+tokenize1 :: ByteString -> ACE+tokenize1 l = case words l of+ [] -> Empty+ (h:ws) -> case (unpack h,ws) of+ ("AS",[cs,rs]) -> AS cs rs+ ("CO",[nm,bss,rs,segs,comp]) -> CO nm bss rs segs comp+ ("BQ",[]) -> BQ+ ("AF",[a,b,c]) -> AF a b c+ ("BS",_) -> BS ws+ ("RD",[a,b,c,d]) -> RD a b c d+ ("QA",[a,b,c,d,e]) -> QA a b c d e+ ("DS",_) -> DS ws+ _ -> Other (h:ws)++-- | Reading an ACE file.+readACE :: FilePath -> IO [[Assembly]]+readACE f = parseit =<< B.readFile f+ where parseit = \s -> case (parse ace f . source f . tokenize) s of+ Left e -> fail (show e)+ Right a -> return a++-- formatError msg = error ("readACE: incorrect format in "++msg)++writeACE :: FilePath -> [Assembly] -> IO ()+writeACE = undefined++-- todo: hWrite etc+