fasta 0.8.0.2 → 0.9.0.0

raw patch · 6 files changed

+351/−55 lines, 6 filesdep +attoparsecdep +pipes-attoparsecPVP ok

version bump matches the API change (PVP)

Dependencies added: attoparsec, pipes-attoparsec

API changes (from Hackage documentation)

Files

• fasta.cabal +3/−1
• src/Data/Fasta/ByteString/Lazy/Parse.hs +90/−16
• src/Data/Fasta/ByteString/Parse.hs +87/−10
• src/Data/Fasta/Text/Lazy/Parse.hs +83/−12
• src/Data/Fasta/Text/Parse.hs +87/−15
• src/Data/Fasta/Text/Types.hs +1/−1

@@ -10,7 +10,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             0.8.0.2+version:             0.9.0.0  -- A short (one-line) description of the package. synopsis:            A simple, mindless parser for fasta files.@@ -82,6 +82,8 @@                      , pipes-group >= 1.0                      , pipes-text >= 0.0                      , pipes-bytestring >= 2.1+                     , attoparsec+                     , pipes-attoparsec                      , lens >= 4.9                      , foldl >= 1.0   

@@ -8,27 +8,34 @@ {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE BangPatterns #-} -module Data.Fasta.ByteString.Lazy.Parse ( parseFasta-                                        , parseCLIPFasta+module Data.Fasta.ByteString.Lazy.Parse ( parsecFasta+                                        , parsecCLIPFasta+                                        , attoFasta+                                        , attoCLIPFasta                                         , pipesFasta+                                        , pipesCLIPFasta                                         , removeNs                                         , removeN                                         , removeCLIPNs ) where  -- Built-in import Data.Char-import Control.Monad (void) import Text.Parsec import Text.Parsec.ByteString.Lazy import qualified Data.Map.Strict as Map+import qualified Data.ByteString as BW import qualified Data.ByteString.Char8 as SB import qualified Data.ByteString.Lazy.Char8 as B+import qualified Control.Applicative as CA+import Control.Monad (void)  -- Cabal+import qualified Data.Attoparsec.ByteString.Char8 as A import Pipes import qualified Pipes.Prelude as P import qualified Pipes.ByteString as PB import qualified Pipes.Group as PG+import qualified Pipes.Attoparsec as PA import Control.Lens (view) import qualified Control.Foldl as FL @@ -71,27 +78,86 @@     spaces     many fastaCLIP --- | Parse a standard fasta file into lazy text sequences-parseFasta :: B.ByteString -> [FastaSequence]-parseFasta = eToV . parse fastaFile "error"+-- | Parse a standard fasta file into+parsecFasta :: B.ByteString -> [FastaSequence]+parsecFasta = eToV . parse fastaFile "error"   where     eToV (Right x) = x     eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x) --- | Parse a CLIP fasta file into lazy text sequences-parseCLIPFasta :: B.ByteString -> CloneMap-parseCLIPFasta = Map.fromList-               . map (\(!x, (!y, !z)) -> ((x, y), z))-               . zip [0..]-               . eToV-               . parse fastaCLIPFile "error"+-- | Parse a CLIP fasta file into+parsecCLIPFasta :: B.ByteString -> CloneMap+parsecCLIPFasta = Map.fromList+                . map (\(!x, (!y, !z)) -> ((x, y), z))+                . zip [0..]+                . eToV+                . parse fastaCLIPFile "error"   where     eToV (Right x) = x     eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x) --- | Parse a standard fasta file into strict text sequences for pipes. This is--- the highly recommeded way of parsing, as it is computationally fast and--- uses memory based on line length+-- | attopares any char but space+anyButSpace :: A.Parser Char+anyButSpace = do+    A.skipSpace+    x <- A.letter_ascii+    A.skipSpace+    return x++-- | attoparsec parser for a fasta type+fasta' :: A.Parser FastaSequence+fasta' = do+    header <- A.takeWhile (\x -> x /= '\n' && x /= '\r')+    A.endOfLine+    fseq <- A.manyTill anyButSpace (void (A.char '>') CA.<|> A.endOfInput)+    return FastaSequence { fastaHeader = B.fromStrict header+                         , fastaSeq = B.pack fseq }++-- | attoparsec parser for a fasta file+fastaFile' :: A.Parser [FastaSequence]+fastaFile' = do+    A.skipSpace+    A.char '>'+    A.many' fasta'++-- | attoparsec parser for a CLIP fasta sequence+fastaCLIP' :: A.Parser FastaSequence+fastaCLIP' = do+    header <- A.takeWhile (\x -> x /= '\n' && x /= '\r')+    A.endOfLine+    fseq <- A.manyTill anyButSpace (void (A.char '>') CA.<|> A.endOfInput)+    return FastaSequence { fastaHeader = B.fromStrict header+                         , fastaSeq = B.pack fseq }++clone' :: A.Parser (Germline, [FastaSequence])+clone' = do+    A.skipSpace+    germline <- fastaCLIP'+    fseqs <- A.manyTill fasta' (void (A.char '>') CA.<|> A.endOfInput)+    return (germline, fseqs)++-- | attoparsec parser for a fasta file+fastaCLIPFile' :: A.Parser [(Germline, [FastaSequence])]+fastaCLIPFile' = do+    A.skipSpace+    A.string ">>"+    A.many' clone'++-- | Parse a standard fasta file+attoFasta :: BW.ByteString -> [FastaSequence]+attoFasta = eToV . A.parseOnly fastaFile'+  where+    eToV (Right x) = x+    eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)++-- | Parse a CLIP fasta file into text sequences+attoCLIPFasta :: BW.ByteString -> [(Germline, [FastaSequence])]+attoCLIPFasta = eToV . A.parseOnly fastaCLIPFile'+  where+    eToV (Right x) = x+    eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)++-- | Parse a standard fasta file into a pipe pipesFasta :: (MonadIO m)            => Producer SB.ByteString m ()            -> Producer FastaSequence m ()@@ -111,6 +177,14 @@                                             . tail                                             . SB.lines                                             $ x }++-- | Parse a CLIP fasta file into strict text sequences for pipes.+pipesCLIPFasta :: (MonadIO m)+               => Producer BW.ByteString m ()+               -> Producer (Germline, [FastaSequence]) m (Either (PA.ParsingError, Producer BW.ByteString m ()) ())+pipesCLIPFasta = PA.parsed clone'+               . PB.drop 2+               . PB.dropWhile (`BW.elem` "\n\r\t ")  -- | Remove Ns from a collection of sequences removeNs :: [FastaSequence] -> [FastaSequence]

@@ -8,9 +8,12 @@ {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE BangPatterns #-} -module Data.Fasta.ByteString.Parse ( parseFasta-                                   , parseCLIPFasta+module Data.Fasta.ByteString.Parse ( parsecFasta+                                   , parsecCLIPFasta+                                   , attoFasta+                                   , attoCLIPFasta                                    , pipesFasta+                                   , pipesCLIPFasta                                    , removeNs                                    , removeN                                    , removeCLIPNs ) where@@ -20,13 +23,18 @@ import Text.Parsec import Text.Parsec.ByteString import qualified Data.Map.Strict as Map+import qualified Data.ByteString as BW import qualified Data.ByteString.Char8 as B+import qualified Control.Applicative as CA+import Control.Monad (void)  -- Cabal+import qualified Data.Attoparsec.ByteString.Char8 as A import Pipes import qualified Pipes.Prelude as P import qualified Pipes.ByteString as PB import qualified Pipes.Group as PG+import qualified Pipes.Attoparsec as PA import Control.Lens (view) import qualified Control.Foldl as FL @@ -69,23 +77,84 @@     many fastaCLIP  -- | Parse a standard fasta file into text sequences-parseFasta :: B.ByteString -> [FastaSequence]-parseFasta = eToV . parse fastaFile "error"+parsecFasta :: B.ByteString -> [FastaSequence]+parsecFasta = eToV . parse fastaFile "error"   where     eToV (Right x) = x     eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)  -- | Parse a CLIP fasta file into text sequences-parseCLIPFasta :: B.ByteString -> CloneMap-parseCLIPFasta = Map.fromList-               . map (\(!x, (!y, !z)) -> ((x, y), z))-               . zip [0..]-               . eToV-               . parse fastaCLIPFile "error"+parsecCLIPFasta :: B.ByteString -> CloneMap+parsecCLIPFasta = Map.fromList+                . map (\(!x, (!y, !z)) -> ((x, y), z))+                . zip [0..]+                . eToV+                . parse fastaCLIPFile "error"   where     eToV (Right x) = x     eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x) +-- | attopares any char but space+anyButSpace :: A.Parser Char+anyButSpace = do+    A.skipSpace+    x <- A.letter_ascii+    A.skipSpace+    return x++-- | attoparsec parser for a fasta type+fasta' :: A.Parser FastaSequence+fasta' = do+    header <- A.takeWhile (\x -> x /= '\n' && x /= '\r')+    A.endOfLine+    fseq <- A.manyTill anyButSpace (void (A.char '>') CA.<|> A.endOfInput)+    return FastaSequence { fastaHeader = header+                         , fastaSeq = B.pack fseq }++-- | attoparsec parser for a fasta file+fastaFile' :: A.Parser [FastaSequence]+fastaFile' = do+    A.skipSpace+    A.char '>'+    A.many' fasta'++-- | attoparsec parser for a CLIP fasta sequence+fastaCLIP' :: A.Parser FastaSequence+fastaCLIP' = do+    header <- A.takeWhile (\x -> x /= '\n' && x /= '\r')+    A.endOfLine+    fseq <- A.manyTill anyButSpace (void (A.char '>') CA.<|> A.endOfInput)+    return FastaSequence { fastaHeader = header+                         , fastaSeq = B.pack fseq }++clone' :: A.Parser (Germline, [FastaSequence])+clone' = do+    A.skipSpace+    germline <- fastaCLIP'+    fseqs <- A.manyTill fasta' (void (A.char '>') CA.<|> A.endOfInput)+    return (germline, fseqs)++-- | attoparsec parser for a fasta file+fastaCLIPFile' :: A.Parser [(Germline, [FastaSequence])]+fastaCLIPFile' = do+    A.skipSpace+    A.string ">>"+    A.many' clone'++-- | Parse a standard fasta file+attoFasta :: B.ByteString -> [FastaSequence]+attoFasta = eToV . A.parseOnly fastaFile'+  where+    eToV (Right x) = x+    eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)++-- | Parse a CLIP fasta file into text sequences+attoCLIPFasta :: B.ByteString -> [(Germline, [FastaSequence])]+attoCLIPFasta = eToV . A.parseOnly fastaCLIPFile'+  where+    eToV (Right x) = x+    eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)+ -- | Parse a standard fasta file into strict text sequences for pipes. This is -- the highly recommeded way of parsing, as it is computationally fast and -- uses memory based on line length@@ -101,6 +170,14 @@   where     toFasta x = FastaSequence { fastaHeader = head . B.lines $ x                               , fastaSeq    = B.concat . tail . B.lines $ x }++-- | Parse a CLIP fasta file into strict text sequences for pipes.+pipesCLIPFasta :: (MonadIO m)+               => Producer B.ByteString m ()+               -> Producer (Germline, [FastaSequence]) m (Either (PA.ParsingError, Producer B.ByteString m ()) ())+pipesCLIPFasta = PA.parsed clone'+               . PB.drop 2+               . PB.dropWhile (`BW.elem` "\n\r\t ")  -- | Remove Ns from a collection of sequences removeNs :: [FastaSequence] -> [FastaSequence]

@@ -1,5 +1,5 @@ -- Parse module.--- By G.W. Schwartz+-- By Gregory W. Schwartz -- {- | Collection of functions for the parsing of a fasta file. Uses the lazy Text type.@@ -8,9 +8,12 @@ {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE BangPatterns #-} -module Data.Fasta.Text.Lazy.Parse ( parseFasta-                                  , parseCLIPFasta+module Data.Fasta.Text.Lazy.Parse ( parsecFasta+                                  , parsecCLIPFasta+                                  , attoFasta+                                  , attoCLIPFasta                                   , pipesFasta+                                  , pipesCLIPFasta                                   , removeNs                                   , removeN                                   , removeCLIPNs ) where@@ -23,12 +26,15 @@ import qualified Data.Map.Strict as Map import qualified Data.Text as ST import qualified Data.Text.Lazy as T+import qualified Control.Applicative as CA  -- Cabal+import qualified Data.Attoparsec.Text as A import Pipes import qualified Pipes.Prelude as P import qualified Pipes.Text as PT import qualified Pipes.Group as PG+import qualified Pipes.Attoparsec as PA import Control.Lens (view) import qualified Control.Foldl as FL @@ -71,16 +77,16 @@     spaces     many fastaCLIP --- | Parse a standard fasta file into lazy text sequences-parseFasta :: T.Text -> [FastaSequence]-parseFasta = eToV . parse fastaFile "error"+-- | Parse a standard fasta file+parsecFasta :: T.Text -> [FastaSequence]+parsecFasta = eToV . parse fastaFile "error"   where     eToV (Right x) = x     eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x) --- | Parse a CLIP fasta file into lazy text sequences-parseCLIPFasta :: T.Text -> CloneMap-parseCLIPFasta = Map.fromList+-- | Parse a CLIP fasta file+parsecCLIPFasta :: T.Text -> CloneMap+parsecCLIPFasta = Map.fromList                . map (\(!x, (!y, !z)) -> ((x, y), z))                . zip [0..]                . eToV@@ -89,9 +95,68 @@     eToV (Right x) = x     eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x) --- | Parse a standard fasta file into strict text sequences for pipes. This is--- the highly recommeded way of parsing, as it is computationally fast and--- uses memory based on line length+-- | attopares any char but space+anyButSpace :: A.Parser Char+anyButSpace = do+    A.skipSpace+    x <- A.letter+    A.skipSpace+    return x++-- | attoparsec parser for a fasta type+fasta' :: A.Parser FastaSequence+fasta' = do+    header <- A.takeWhile (not . A.isEndOfLine)+    A.endOfLine+    fseq <- A.manyTill anyButSpace (void (A.char '>') CA.<|> A.endOfInput)+    return FastaSequence { fastaHeader = T.fromStrict header+                         , fastaSeq = T.pack fseq }++-- | attoparsec parser for a fasta file+fastaFile' :: A.Parser [FastaSequence]+fastaFile' = do+    A.skipSpace+    A.char '>'+    A.many' fasta'++-- | attoparsec parser for a CLIP fasta sequence+fastaCLIP' :: A.Parser FastaSequence+fastaCLIP' = do+    header <- A.takeWhile (not . A.isEndOfLine)+    A.endOfLine+    fseq <- A.manyTill anyButSpace (void (A.char '>') CA.<|> A.endOfInput)+    return FastaSequence { fastaHeader = T.fromStrict header+                         , fastaSeq = T.pack fseq }++clone' :: A.Parser (Germline, [FastaSequence])+clone' = do+    A.skipSpace+    germline <- fastaCLIP'+    fseqs <- A.manyTill fasta' (void (A.char '>') CA.<|> A.endOfInput)+    return (germline, fseqs)++-- | attoparsec parser for a fasta file+fastaCLIPFile' :: A.Parser [(Germline, [FastaSequence])]+fastaCLIPFile' = do+    A.skipSpace+    A.string ">>"+    A.many' clone'++-- | Parse a standard fasta file+attoFasta :: ST.Text -> [FastaSequence]+attoFasta = eToV . A.parseOnly fastaFile'+  where+    eToV (Right x) = x+    eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)++-- | Parse a CLIP fasta file+attoCLIPFasta :: ST.Text -> [(Germline, [FastaSequence])]+attoCLIPFasta = eToV . A.parseOnly fastaCLIPFile'+  where+    eToV (Right x) = x+    eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)++-- | Parse a standard fasta file into a pipe pipesFasta :: (MonadIO m)            => Producer ST.Text m ()            -> Producer FastaSequence m ()@@ -108,6 +173,12 @@                                             . tail                                             . ST.lines                                             $ x }++-- | Parse a CLIP fasta file into a pipe+pipesCLIPFasta :: (MonadIO m)+               => Producer ST.Text m ()+               -> Producer (Germline, [FastaSequence]) m (Either (PA.ParsingError, Producer ST.Text m ()) ())+pipesCLIPFasta = PA.parsed clone' . PT.drop 2 . (>-> PT.stripStart)  -- | Remove Ns from a collection of sequences removeNs :: [FastaSequence] -> [FastaSequence]

@@ -8,9 +8,12 @@ {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE BangPatterns #-} -module Data.Fasta.Text.Parse ( parseFasta-                             , parseCLIPFasta+module Data.Fasta.Text.Parse ( parsecFasta+                             , parsecCLIPFasta+                             , attoFasta+                             , attoCLIPFasta                              , pipesFasta+                             , pipesCLIPFasta                              , removeNs                              , removeN                              , removeCLIPNs ) where@@ -21,12 +24,16 @@ import Text.Parsec.Text import qualified Data.Map.Strict as Map import qualified Data.Text as T+import qualified Control.Applicative as CA+import Control.Monad (void)  -- Cabal+import qualified Data.Attoparsec.Text as A import Pipes import qualified Pipes.Prelude as P import qualified Pipes.Text as PT import qualified Pipes.Group as PG+import qualified Pipes.Attoparsec as PA import Control.Lens (view) import qualified Control.Foldl as FL @@ -68,27 +75,86 @@     spaces     many fastaCLIP --- | Parse a standard fasta file into text sequences-parseFasta :: T.Text -> [FastaSequence]-parseFasta = eToV . parse fastaFile "error"+-- | Parse a standard fasta file+parsecFasta :: T.Text -> [FastaSequence]+parsecFasta = eToV . parse fastaFile "error"   where     eToV (Right x) = x     eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x) --- | Parse a CLIP fasta file into text sequences-parseCLIPFasta :: T.Text -> CloneMap-parseCLIPFasta = Map.fromList-               . map (\(!x, (!y, !z)) -> ((x, y), z))-               . zip [0..]-               . eToV-               . parse fastaCLIPFile "error"+-- | Parse a CLIP fasta file+parsecCLIPFasta :: T.Text -> CloneMap+parsecCLIPFasta = Map.fromList+                . map (\(!x, (!y, !z)) -> ((x, y), z))+                . zip [0..]+                . eToV+                . parse fastaCLIPFile "error"   where     eToV (Right x) = x     eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x) --- | Parse a standard fasta file into strict text sequences for pipes. This is--- the highly recommeded way of parsing, as it is computationally fast and--- uses memory based on line length+-- | attopares any char but space+anyButSpace :: A.Parser Char+anyButSpace = do+    A.skipSpace+    x <- A.letter+    A.skipSpace+    return x++-- | attoparsec parser for a fasta type+fasta' :: A.Parser FastaSequence+fasta' = do+    header <- A.takeWhile (not . A.isEndOfLine)+    A.endOfLine+    fseq <- A.manyTill anyButSpace (void (A.char '>') CA.<|> A.endOfInput)+    return FastaSequence { fastaHeader = header+                         , fastaSeq = T.pack fseq }++-- | attoparsec parser for a fasta file+fastaFile' :: A.Parser [FastaSequence]+fastaFile' = do+    A.skipSpace+    A.char '>'+    A.many' fasta'++-- | attoparsec parser for a CLIP fasta sequence+fastaCLIP' :: A.Parser FastaSequence+fastaCLIP' = do+    header <- A.takeWhile (not . A.isEndOfLine)+    A.endOfLine+    fseq <- A.manyTill anyButSpace (void (A.char '>') CA.<|> A.endOfInput)+    return FastaSequence { fastaHeader = header+                         , fastaSeq = T.pack fseq }++clone' :: A.Parser (Germline, [FastaSequence])+clone' = do+    A.skipSpace+    germline <- fastaCLIP'+    fseqs <- A.manyTill fasta' (void (A.char '>') CA.<|> A.endOfInput)+    return (germline, fseqs)++-- | attoparsec parser for a fasta file+fastaCLIPFile' :: A.Parser [(Germline, [FastaSequence])]+fastaCLIPFile' = do+    A.skipSpace+    A.string ">>"+    A.many' clone'++-- | Parse a standard fasta file+attoFasta :: T.Text -> [FastaSequence]+attoFasta = eToV . A.parseOnly fastaFile'+  where+    eToV (Right x) = x+    eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)++-- | Parse a CLIP fasta file+attoCLIPFasta :: T.Text -> [(Germline, [FastaSequence])]+attoCLIPFasta = eToV . A.parseOnly fastaCLIPFile'+  where+    eToV (Right x) = x+    eToV (Left x)  = error ("Unable to parse fasta file\n" ++ show x)++-- | Parse a standard fasta file into a pipe pipesFasta :: (MonadIO m) => Producer T.Text m () -> Producer FastaSequence m () pipesFasta p = FL.purely PG.folds FL.mconcat ( view (PT.splits '>')                                              . PT.drop (1 :: Int)@@ -97,6 +163,12 @@   where     toFasta x = FastaSequence { fastaHeader = head . T.lines $ x                               , fastaSeq    = T.concat . tail . T.lines $ x }++-- | Parse a CLIP fasta file into a pipe+pipesCLIPFasta :: (MonadIO m)+               => Producer T.Text m ()+               -> Producer (Germline, [FastaSequence]) m (Either (PA.ParsingError, Producer T.Text m ()) ())+pipesCLIPFasta = PA.parsed clone' . PT.drop 2 . (>-> PT.stripStart)  -- | Remove Ns from a collection of sequences removeNs :: [FastaSequence] -> [FastaSequence]

@@ -1,5 +1,5 @@ -- Types module.--- By G.W. Schwartz+-- By Gregory W. Schwartz -- {- | Collects all application specific types. Used here for Text. -}