bio 0.3.3.1 → 0.3.3.2

raw patch · 6 files changed

+19/−10 lines, 6 filesdep −interlude

Dependencies removed: interlude

Files

• Bio/Alignment/ACE.hs +1/−2
• Bio/Alignment/BlastXML.hs +7/−3
• Bio/Sequence.hs +3/−0
• Bio/Sequence/Entropy.hs +1/−1
• Bio/Sequence/Fasta.hs +4/−1
• bio.cabal +3/−3

@@ -28,8 +28,7 @@  module Bio.Alignment.ACE (readACE, writeACE, Assembly(..), ptest, reads ) where -#include <interlude.h>-import Interlude hiding (lines,words,readFile,unwords -- ByteString clashes+import Prelude   hiding (lines,words,readFile,unwords -- ByteString clashes                         ,reads,pred                   -- Assembly clash                         ) 

@@ -1,6 +1,6 @@ -- Parse blast XML output using tagsoup -module Bio.Alignment.BlastXML where+module Bio.Alignment.BlastXML (readXML) where  import Bio.Alignment.BlastData @@ -23,6 +23,7 @@                   in  rest `par` first : if null rest then [] else breaks p rest breaks _ []     = [] +getFrom :: [Tag] -> String -> String getFrom list tag = let xs = sections (isTagOpenName tag) list                     in if null xs || null (head xs) || (null . drop 1 . head) xs                        then error ("Couldn't find tag '"++show tag++"' in\n"++showSome list)@@ -31,6 +32,7 @@                              x -> error ("Unexpeced tag: "++ show x)  -- Use pattern match since 'length' is strict, defeating the purpose.+showSome :: [Tag] -> String showSome a@(_:_:_:_:_:_:_) = (init . show . take 5 $ a)++" ... ]" showSome a                 = show a @@ -64,6 +66,7 @@              }     where get = getFrom hs + hsp2match :: [Tag] -> BlastMatch hsp2match ms = BlastMatch                { bits   = read $ get "Hsp_bit-score"@@ -78,13 +81,14 @@                          [] -> mkFrame $ get "Hsp_query-frame"                          [(_o:TagText hf:_c)] -> case sections (isTagOpenName "Hsp_query-frame") ms of                                                     [] -> mkFrame hf-                                                   [(_o:TagText qf:_c)] -> mkStrands hf qf+                                                   [(__o:TagText qf:__c)] -> mkStrands hf qf+                                                   e -> error ("hsp2match: should be tagopen/text/close:\n"++show e)                          e -> error ("hsp2match: failed to determine frame:\n"++show e)                }     where get = getFrom ms           mkFrame f = Frame (strand' $ signum $ read f) (abs $ read f)           mkStrands h q = Strands (strand' $ read h) (strand' $ read q)           strand' s = case s of 1 -> Plus; -1 -> Minus-                                _ -> error ("Strand must be +1 or -1, but was"++show s)+                                _ -> error ("Strand must be +1 or -1, but was: "++show s)  

@@ -42,6 +42,9 @@     -- | Packing words from sequences into integral data types      , HashF (..)     , contigous, rcontig, rcpacked++    -- * Entropy calculations+    , KWords(..), entropy     ) where  -- basic sequence data structures

@@ -1,4 +1,4 @@-module Bio.Sequence.Entropy where+module Bio.Sequence.Entropy (KWords(..), entropy) where  import Data.List 

@@ -97,6 +97,7 @@           | B.length y /= B.length z   = error ("mismatching sequence and quality lengths:"                                                 ++ show (seqlabel s1,B.length y,B.length z))           | otherwise   = Seq x y (Just z)+      mkseq _ _ = error "readFastaQual: could not combine Fasta and Qual information"   return $ zipWith mkseq ss qs  -- | Write sequence and quality data simulatnously@@ -144,7 +145,7 @@   wHead h l   let qls = splitsAt 20 q       qs = B.pack . unwords . map show . BB.unpack-  mapM_ ((\l -> B.hPut h l >> B.hPut h (B.pack "\n")) . qs) qls+  mapM_ ((\l' -> B.hPut h l' >> B.hPut h (B.pack "\n")) . qs) qls wQual _ (Seq _ _ Nothing) = return ()  -- ByteString operations@@ -179,6 +180,7 @@ mkSeqs :: [ByteString] -> [Sequence] mkSeqs = map mkSeq . blocks +mkSeq :: [ByteString] -> Sequence mkSeq (l:ls) = Seq (B.drop 1 l) (B.concat $ takeWhile isSeq ls) Nothing     where isSeq s = (not . B.null) s && ((flip elem) (['A'..'Z']++['a'..'z']) . B.head) s mkSeq [] = error "empty input to mkSeq"@@ -187,6 +189,7 @@ mkQual = map f . blocks     where f (l:ls) = Seq (B.drop 1 l) B.empty                      (Just $ BB.pack (map int (B.words $ B.unlines ls)))+          f [] = error "mkQual: empty quality data"           int = fromIntegral . fst . fromJust' . B.readInt           fromJust' = maybe (error "Error in qual format") id 

@@ -1,5 +1,5 @@ Name:                bio-Version:             0.3.3.1+Version:             0.3.3.2 License:             LGPL License-file:        LICENSE Author:              Ketil Malde@@ -19,13 +19,13 @@                      output parsing.  Partly implemented single linkage clustering, and                      multiple alignment.                      .-                     The Darcs repository is at: <http://malde.org/~ketil/bio>.+                     The Darcs repository is at: <http://malde.org/~ketil/biohaskell/biolib>. Homepage:            http://malde.org/~ketil/  Tested-With:         GHC==6.8.2 Build-Type:          Simple Build-Depends:       base>3, QuickCheck<2, binary, tagsoup>=0.4, bytestring,-                     containers, array, interlude, parallel, parsec+                     containers, array, parallel, parsec -- add fps for ghc 6.4.2; change imports in Bio/Sequence/TwoBit.hs if you want QC 2  -- We omit the debian/ and Test/ files because those are for development, not installation.