biofastq (empty) → 0.1

raw patch · 3 files changed

+130/−0 lines, 3 filesdep +basedep +biocoredep +bytestringsetup-changed

Dependencies added: base, biocore, bytestring

Files

• Setup.hs +2/−0
• biofastq.cabal +18/−0
• src/Bio/Sequence/FastQ.hs +110/−0

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

@@ -0,0 +1,18 @@+Name:          biofastq+Version:       0.1+License:       LGPL+Cabal-Version: >= 1.6+Build-Type:    Simple+Category:      Bioinformatics+Author:        Ketil Malde+Maintainer:    Ketil Malde <ketil@malde.org>+Synopsis:      A library for reading FASTQ files+Homepage:      http://biohaskell.org/++Library+    Hs-Source-Dirs:  src+    Exposed-Modules: Bio.Sequence.FastQ+    Ghc-Options:     -Wall+    Build-Depends:   base >= 4 && < 5, bytestring >= 0.9, biocore >= 0.2++

@@ -0,0 +1,110 @@+{- |+   Module: Bio.Sequence.FastQ++   Support the FastQ format that combines sequence and quality. See:++   * <http://www.bioperl.org/wiki/FASTQ_sequence_format>++   Of course, this is yet another vaguely defined pseudo-standard with+   conflicting definitions.  Of course Solexa had to go and invent not one, but two +   different, and indistinguishably so, ways to do it:++   * <http://www.bcgsc.ca/pipermail/ssrformat/2007-March/000137.html>++   * <http://maq.sourceforge.net/fastq.shtml>++   * <http://en.wikipedia.org/wiki/FASTQ_format>++   Sanger-style FastQ-format is supported with the (h)read/writeSangerQ functions,+   and the new Illumina/Solexa-style with (h)read/writeIllumina.++   As far as I know, FastQ is only used for nucleotide sequences, never amino acid.+-}+++module Bio.Sequence.FastQ+    (+     -- * Reading FastQ+    readFastQ, hReadFastQ, parse+     -- * Writing FastQ+    , writeFastQ, hWriteFastQ++    -- * use Sanger-style quality information+    , readSangerQ, hReadSangerQ+    , writeSangerQ, hWriteSangerQ+    +    -- * use Illumina (>v1.3)-style quality information+    , readIllumina, hReadIllumina+    , writeIllumina, hWriteIllumina+    ) where++import System.IO+import qualified Data.ByteString.Lazy.Char8 as B+import qualified Data.ByteString.Lazy as BB+import Data.List (unfoldr)+import Bio.Core.Sequence++data Sequence = Seq SeqLabel SeqData QualData++instance BioSeq Sequence where+  seqlabel (Seq sl _ _) = sl+  seqdata (Seq _ sd _) = sd  +  seqlength = Offset . B.length . unSD . seqdata -- should be default+  +instance BioSeqQual Sequence where+  seqqual (Seq _ _ q) = q+  +{-# DEPRECATED readFastQ, hReadFastQ, writeFastQ, hWriteFastQ  "FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead" #-}++readSangerQ, readIllumina :: FilePath -> IO [Sequence]+readSangerQ = readFastQ+readIllumina f = addQual (negate 31) `fmap` readFastQ f++hReadSangerQ, hReadIllumina :: Handle -> IO [Sequence]+hReadSangerQ = hReadFastQ+hReadIllumina h = addQual (negate 31) `fmap` hReadFastQ h++writeSangerQ, writeIllumina :: FilePath -> [Sequence] -> IO ()+writeSangerQ = writeFastQ+writeIllumina f = writeFastQ f . addQual 31 ++hWriteSangerQ, hWriteIllumina :: Handle -> [Sequence] -> IO ()+hWriteSangerQ = hWriteFastQ+hWriteIllumina h = hWriteFastQ h . addQual 31++addQual :: Qual -> [Sequence] -> [Sequence]+addQual (Qual q) = map (\(Seq h d mq) -> (Seq h d $ qmap (+q) mq))+  where qmap f (QualData qd) = QualData (BB.map f qd)++readFastQ :: FilePath -> IO [Sequence]+readFastQ f = (go . B.lines) `fmap` B.readFile f++hReadFastQ :: Handle -> IO [Sequence]+hReadFastQ h = (go . B.lines) `fmap` B.hGetContents h++go :: [B.ByteString] -> [Sequence]+go = map (either error id) . unfoldr parse++-- | Parse one FastQ entry, suitable for using in 'unfoldr' over+--   'B.lines' from a file+parse :: [B.ByteString] -> Maybe (Either String (Sequence), [B.ByteString])+parse (h1:sd:h2:sq:rest) =+    case (B.uncons h1,B.uncons h2) of+      -- The fast path: four-line format+      (Just ('@',h1name), Just ('+',h2name))+          | h1name == h2name || B.null h2name+            -> Just (Right $ Seq (SeqLabel h1name) (SeqData sd) (QualData (BB.map (subtract 33) sq)), rest)+          | otherwise+            -> Just (Left $ "Bio.Sequence.FastQ: name mismatch:" ++ showStanza, rest)+      _     -> Just (Left $ "Bio.Sequence.FastQ: illegal FastQ format:" ++ showStanza, rest)+    where showStanza = unlines $ map B.unpack [ h1, sd, h2, sq ]+parse [] = Nothing+parse fs = let showStanza = unlines (map B.unpack fs)+               err = Left $ "Bio.Sequence.FastQ: illegal number of lines in FastQ format: " ++ showStanza+           in Just (err, [])++writeFastQ :: FilePath -> [Sequence] -> IO ()+writeFastQ f = B.writeFile f . B.concat . map toFastQ++hWriteFastQ :: Handle -> [Sequence] -> IO ()+hWriteFastQ h = B.hPut h . B.concat . map toFastQ