ViennaRNAParser 1.3.0 → 1.3.1

raw patch · 4 files changed

+54/−32 lines, 4 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• ViennaRNAParser.cabal +3/−3
• changelog +3/−0
• src/Bio/RNAcodeData.hs +3/−2
• src/Bio/RNAcodeParser.hs +45/−27

@@ -5,7 +5,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.3.0+version:             1.3.1 synopsis:            Libary for parsing ViennaRNA package output description:         Currently contains parsers and datatypes for: RNAalifold, RNAcode, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz. 		     .@@ -30,8 +30,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.3.0-  tag:      1.3.0+  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.3.1+  tag:      1.3.1  library   -- Modules exported by the library.

@@ -1,4 +1,7 @@ -*-change-log-*-+1.3.1 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 23. October 2016+        * Improvements to RNAcode parser,+	* Improvements to travis testing 1.3.0 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 6. September 2016         * Added support for new prefilter fields in RNAplex output  1.2.8 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 11. February 2016

@@ -22,8 +22,9 @@ data RNAcodeHit = RNAcodeHit   {      hss :: Int,-    frame :: Double,-    length :: Int,+    strand :: Char,+    frame :: Int,+    hitLength :: Int,     from :: Int,     to :: Int,     name :: String,

@@ -19,6 +19,7 @@ import qualified Control.Exception.Base as CE import Text.Parsec.Language (haskell) import Control.Applicative ((<*>),(<$>),(<$),pure)+import Text.Parsec.Numbers      -- | Run external RNAcode command and read the output into the corresponding datatype systemRNAcode :: String -> String -> String -> IO ExitCode@@ -33,21 +34,29 @@ -- | Parse the input as RNAcodeHit genParseRNAcodeTabularHit :: GenParser Char st RNAcodeHit genParseRNAcodeTabularHit = do-  _hss <- natural haskell-  _frame <- integer haskell-  _length <- natural haskell-  _from <- natural haskell-  _to <- natural haskell-  _name <- identifier haskell-  --_name <- identifier haskell+  _hss <- parseIntegral+  tab+  _strand <- oneOf "+-"+  tab+  _frame <- parseIntegral+  tab          +  _length <- parseIntegral+  tab+  _from <- parseIntegral+  tab         +  _to <-parseIntegral+  tab   _name <- many1 (oneOf "AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz1234567890_-")-  string ("\t")-  _start <- natural haskell-  _end <- natural haskell-  _score <- many1 (oneOf "1234567890e.-+")-  many space-  _pvalue <- float haskell-  return $ RNAcodeHit (fromInteger _hss) (fromInteger _frame) (fromInteger _length) (fromInteger _from) (fromInteger _to) _name (fromInteger _start) (fromInteger _end) (read _score ::Double) _pvalue +  tab+  _start <- parseIntegral+  tab          +  _end <- parseIntegral+  tab        +  _score <- parseFloat+  tab          +  _pvalue <- parseFloat+  newline+  return $ RNAcodeHit  _hss _strand _frame _length _from _to _name _start _end _score _pvalue    -- | Parse the input as RNAcode datatype@@ -82,20 +91,29 @@ genParseRNAcodeHit :: GenParser Char st RNAcodeHit genParseRNAcodeHit = do   many (char ' ')-  _hss <- natural haskell-  _frame <- integer haskell-  _length <- natural haskell-  _from <- natural haskell-  _to <- natural haskell-  --_name <- identifier haskell+  _hss <- parseIntegral+  tab+  _strand <- oneOf "+-"        +  tab+  _frame <- parseIntegral+  tab+  _length <- parseIntegral+  tab+  _from <- parseIntegral+  tab+  _to <- parseIntegral+  tab   _name <- many1 (oneOf "AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz1234567890_-")-  string ("\t")-  _start <- natural haskell-  _end <- natural haskell-  _score <- float haskell-  _pvalue <- many1 (try (choice [digit,char '.']))+  tab+  _start <- parseIntegral+  tab+  _end <- parseIntegral+  tab        +  _score <- parseFloat+  tab          +  _pvalue <- parseFloat   newline-  return $ RNAcodeHit (fromInteger _hss) (fromInteger _frame) (fromInteger _length) (fromInteger _from) (fromInteger _to) _name (fromInteger _start) (fromInteger _end) _score (read _pvalue :: Double)+  return $ RNAcodeHit  _hss _strand _frame _length _from _to _name _start _end _score _pvalue   -- | parse RNAcode from input string parseRNAcode :: String -> Either ParseError RNAcode@@ -109,7 +127,7 @@  -- | parse RNAcode from input string parseRNAcodeTabular :: String -> Either ParseError RNAcode-parseRNAcodeTabular = parse genParseRNAcodeTabular "parseRNAcode" +parseRNAcodeTabular = parse genParseRNAcodeTabular "parseRNAcodeTabular"   -- | parse RNAcode from input filePath                       readRNAcodeTabular :: String -> IO (Either ParseError RNAcode)