biocore 0.3 → 0.3.1

raw patch · 2 files changed

+12/−9 lines, 2 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• biocore.cabal +1/−1
• src/Bio/Core/Sequence.hs +11/−8

@@ -1,5 +1,5 @@ Name:      biocore-Version:   0.3+Version:   0.3.1 License:   LGPL  Cabal-Version:       >= 1.6

@@ -79,23 +79,26 @@ --   represents a biological sequence should implement it. class BioSeq s where   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. --- | Deprecated.  Instead, use 'seqid' if you want the unique ID, or ---   'seqheader' if you want the FASTA style header with ID and comments.-seqlabel  :: BioSeq s => s -> SeqLabel-seqlabel = seqid+  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 ">"@@ -109,7 +112,7 @@ -- | 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 ">"@@ -117,7 +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)]