bio 0.4.4 → 0.4.5

raw patch · 3 files changed

+18/−21 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• Bio/Alignment/PSL.hs +16/−16
• Bio/Sequence/Fasta.hs +1/−4
• bio.cabal +1/−1

@@ -8,6 +8,7 @@  import qualified Data.ByteString.Lazy.Char8 as B import Data.ByteString.Lazy.Char8 (ByteString)+import Data.List (intersperse)  -- encodes the fields in a Blat PSL record -- NB! laziness issues, if not fully evaluated, this will hang onto the input.@@ -17,24 +18,16 @@                  , qname :: ByteString, qsize, qstart, qend :: Int                  , tname :: ByteString, tsize, tstart, tend :: Int                  , blockcount :: Int, blocksizes, qstarts, tstarts :: [Int]-                 } deriving Show-{--sread :: ByteString -> Strand-sread b = case B.uncons b of -  Just ('-',_) -> Minus-  Just ('+',_) -> Plus-  _ -> error ("Cant't parse '"++B.unpack b++"' as strand")+                 } deriving (Eq) -swrite :: Strand -> ByteString-swrite Minus = B.pack "-"-swrite Plus  = B.pack "+"--}+instance Show PSL where +  show = B.unpack . unparsePSL . return  readPSL :: FilePath -> IO [PSL] readPSL f = parsePSL `fmap` B.readFile f  writePSL :: FilePath -> [PSL] -> IO ()-writePSL f =  B.writeFile f . unparsePSL+writePSL f =  B.writeFile f . B.append pslHeader . unparsePSL   parsePSL :: ByteString -> [PSL] parsePSL s = map parseLine $ B.lines $ dropHeader@@ -51,11 +44,18 @@   unparsePSL :: [PSL] -> ByteString-unparsePSL bs = addHeader $ B.unlines $ map format1 bs-  where addHeader = B.append pslHeader-        format1 :: PSL -> ByteString-        format1 = undefined+unparsePSL = B.unlines . map format1+  where format1 :: PSL -> ByteString+        format1 (PSL m mm rm nc qc ql tgc tgl st qn qsz qst qed tn tsz tst ted bc bs qss tss) = +          B.concat $ intersperse tab $ (map showint [m, mm, rm, nc, qc, ql, tgc, tgl]+                                        ++[st,qn]++map showint [qsz,qst,qed]+                                        ++[tn]   ++map showint [tsz,tst,ted]+                                        ++[showint bc]++map showlist [bs,qss,tss])+        tab = B.pack "\t"+        showint  = B.pack . show+        showlist = B.pack . concat . map (++",") . map show +pslHeader :: ByteString pslHeader = B.pack ("psLayout version 3\n\n"                     ++"match\tmis- \trep. \tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ        \tQ   \tQ    \tQ  \tT        \tT   \tT    \tT  \tblock\tblockSizes \tqStarts\t tStarts\n"                     ++"     \tmatch\tmatch\t   \tcount\tbases\tcount\tbases\t      \tname     \tsize\tstart\tend\tname     \tsize\tstart\tend\tcount\n"

@@ -30,10 +30,7 @@  -- import Data.Char (isSpace) import Data.List (groupBy,intersperse)-import Data.Int-import Data.Maybe import System.IO-import Control.Monad  import qualified Data.ByteString.Lazy.Char8 as B import qualified Data.ByteString.Lazy as BB@@ -175,7 +172,7 @@ -- | Split lines into blocks starting with '>' characters --   Filter out # comments (but not semicolons?) blocks :: [ByteString] -> [[ByteString]]-blocks = groupBy (const (('>' /=) . B.head)) . filter ((/='#') . B.head) . filter (not . B.null)+blocks = groupBy (const (('>' /=) . B.head)) . filter ((/='#') . B.head) . dropWhile (('>' /=) . B.head) . filter (not . B.null)  countSeqs :: FilePath -> IO Int countSeqs f = do

@@ -1,5 +1,5 @@ Name:                bio-Version:             0.4.4+Version:             0.4.5 License:             LGPL License-file:        LICENSE Author:              Ketil Malde