biocore 0.2 → 0.3.1

raw patch · 2 files changed

Files

biocore.cabal +2/−2
src/Bio/Core/Sequence.hs +61/−17

biocore.cabal view

@@ -1,5 +1,5 @@ Name:      biocore-Version:   0.2+Version:   0.3.1 License:   LGPL  Cabal-Version:       >= 1.6@@ -22,7 +22,7 @@   Location: http://malde.org/~ketil/biohaskell/biocore/  Library-  Build-Depends:     base >= 3 && < 5, bytestring+  Build-Depends:     base >= 3 && < 5, bytestring, stringable   Exposed-Modules:   Bio.Core, Bio.Core.Sequence, Bio.Core.Strand   Ghc-Options:       -Wall   Hs-Source-Dirs:    src

src/Bio/Core/Sequence.hs view

@@ -6,7 +6,8 @@     is available).      The data types are mostly wrappers from lazy bytestrings from-    'Data.ByteString.Lazy' and 'Data.ByteString.Lazy.Char8'.+    'Data.ByteString.Lazy' and 'Data.ByteString.Lazy.Char8', but most users+    of this module should not need to access the underlying data types directly. -}  {-# LANGUAGE GeneralizedNewtypeDeriving, DeriveDataTypeable #-}@@ -20,7 +21,10 @@   BioSeq (..), BioSeqQual (..),    -- * Helper functions-  toFasta, toFastaQual, toFastQ+  toFasta, toFastaQual, toFastQ,++  module Data.Stringable+   ) where  import qualified Data.ByteString.Lazy.Char8 as LC@@ -29,46 +33,86 @@ import Data.Typeable (Typeable) import Data.Word import Data.String+import Data.Stringable hiding (length)+import Data.Monoid  -- | Sequence data are lazy bytestrings of ASCII characters.-newtype SeqData  = SeqData { unSD :: LC.ByteString } deriving (Eq,Ord,IsString,Show,Typeable)+newtype SeqData  = SeqData { unSD :: LC.ByteString }+                 deriving (Eq,Ord,IsString,Show,Typeable,Stringable) +instance Monoid SeqData where+  mempty = SeqData mempty+  mappend (SeqData s1) (SeqData s2) = SeqData (mappend s1 s2)+  mconcat = SeqData . mconcat . map unSD+ -- | Sequence data are lazy bytestrings of ASCII characters.-newtype SeqLabel = SeqLabel { unSL :: LC.ByteString } deriving (Eq,Ord,IsString,Show,Typeable)+newtype SeqLabel = SeqLabel { unSL :: LC.ByteString }+                 deriving (Eq,Ord,IsString,Show,Typeable,Stringable) +instance Monoid SeqLabel where+  mempty = SeqLabel mempty+  mappend (SeqLabel s1) (SeqLabel s2) = let+    (i1:r1) = LC.words s1+    (i2:r2) = LC.words s2+    sid = mconcat [i1,(LC.pack ":"),i2]+    in SeqLabel (LC.unwords ([sid]++r1++[LC.pack ":"]++r2))+  -- mconcat default+ -- | A quality value is in the range 0..255.-newtype Qual     = Qual { unQual :: Word8 } deriving (Show,Eq,Ord,Num)+newtype Qual     = Qual { unQual :: Word8 }+                 deriving (Show,Eq,Ord,Num,Enum,Real,Integral,Typeable)  -- | Quality data are lazy bytestrings of 'Qual's.-newtype QualData = QualData { unQD :: L.ByteString } deriving (Eq,Ord,Show,Typeable)+newtype QualData = QualData { unQD :: L.ByteString }+                 deriving (Eq,Ord,Show,Typeable,Stringable) +instance Monoid QualData where+  mempty = QualData mempty+  mappend (QualData s1) (QualData s2) = QualData (mappend s1 s2)+  mconcat = QualData . mconcat . map unQD+ -- | An 'Offset' is a zero-based index into a sequence-newtype Offset   = Offset { unOff :: Int64 } deriving (Show,Eq,Ord,Num,Enum,Real,Integral,Typeable)+newtype Offset   = Offset { unOff :: Int64 }+                 deriving (Show,Eq,Ord,Num,Enum,Real,Integral,Typeable)  -- | The 'BioSeq' class models sequence data, and any data object that --   represents a biological sequence should implement it. class BioSeq s where-  seqlabel  :: s -> SeqLabel-  seqdata   :: s -> SeqData-  seqlength :: s -> Offset+  seqid     :: s -> SeqLabel -- ^ Sequence identifier (typically first word of the header)+  seqid = seqlabel+  seqheader :: s -> SeqLabel -- ^ Sequence header (may contain whitespace), by convention the+                             --   first word matches the 'seqid'+  seqheader = seqlabel+  seqdata   :: s -> SeqData  -- ^ Sequence data+  seqlength :: s -> Offset   -- ^ Sequence length +--  slice     :: s -> (Offset,Offset) -> s  -- ^ Cut a slice of a sequence.+--  copy      :: s -> s                     -- ^ Create a copy of a sequence.++  seqlabel  :: s -> SeqLabel -- ^ Deprecated.  Instead, use 'seqid' if you +                             -- want the unique ID, or 'seqheader' if you +                             -- want the FASTA style header with ID and comments.+  seqlabel = seqid ++{-# DEPRECATED seqlabel "Warning: 'seqlabel' is deprecated, use 'seqid' or 'seqheader' instead." #-}+ -- | Any 'BioSeq' can be formatted as Fasta, 60-char lines. toFasta :: BioSeq s => s -> LC.ByteString -- any kind of string-like data type?  Use builder?-toFasta s = LC.concat (gt:unSL (seqlabel s):nl:wrap (unSD $ seqdata s))+toFasta s = LC.concat (gt:unSL (seqheader s):nl:wrap (unSD $ seqdata s))   where wrap x = if LC.null x then [] else let (ln,rest) = LC.splitAt 60 x in ln : nl : wrap rest         nl = LC.pack "\n"         gt = LC.pack ">"-                                         --- | The BioSeqQual class extends BioSeq with quality data.  Any correspondig data object++-- | The BioSeqQual class extends 'BioSeq' with quality data.  Any correspondig data object --   should be an instance, this will allow Fasta formatted quality data 'toFastaQual', as --   well as the combined FastQ format (via 'toFastQ'). class BioSeq sq => BioSeqQual sq where   seqqual  :: sq -> QualData --- | Output Fasta-formatted quality data (.qual files), where quality values are output as +-- | Output Fasta-formatted quality data (.qual files), where quality values are output as --   whitespace-separated integers. toFastaQual :: BioSeqQual s => s -> LC.ByteString-toFastaQual s = LC.concat (gt:unSL (seqlabel s):nl:wrap (L.unpack $ unQD $ seqqual s))+toFastaQual s = LC.concat (gt:unSL (seqheader s):nl:wrap (L.unpack $ unQD $ seqqual s))   where wrap x = if null x then [] else let (ln,rest) = splitAt 20 x in LC.pack (unwords $ map show ln) : nl : wrap rest         nl = LC.pack "\n"         gt = LC.pack ">"@@ -76,7 +120,7 @@ -- | Output FastQ-formatted data.  For simplicity, only the Sanger quality format is supported, --   and only four lines per sequence (i.e. no line breaks in sequence or quality data). toFastQ :: BioSeqQual s => s -> LC.ByteString-toFastQ s = LC.unlines [LC.cons '@' (unSL $ seqlabel s)+toFastQ s = LC.unlines [LC.cons '@' (unSL $ seqid s)                        , unSD (seqdata s)-                       , LC.cons '+' (unSL $ seqlabel s)+                       , LC.cons '+' (unSL $ seqid s)                        , L.map (+33) (unQD $ seqqual s)]