ViennaRNAParser 1.2.6 → 1.2.7

raw patch · 6 files changed

+164/−9 lines, 6 filesdep +transformersPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: transformers

API changes (from Hackage documentation)

Files

• README.md +1/−1
• ViennaRNAParser.cabal +7/−5
• changelog +4/−2
• src/Bio/RNAcodeData.hs +35/−0
• src/Bio/RNAcodeParser.hs +112/−0
• src/Bio/ViennaRNAParser.hs +5/−1

@@ -1,7 +1,7 @@ ViennaRNAParser [![Hackage](https://img.shields.io/hackage/v/ViennaRNAParser.svg)](https://hackage.haskell.org/package/ViennaRNAParser) [![Build Status](https://travis-ci.org/eggzilla/ViennaRNAParser.svg)](https://travis-ci.org/eggzilla/ViennaRNAParser) ============= -Currently contains parsers and datatypes for: RNAalifold, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz.+Currently contains parsers and datatypes for: RNAalifold, RNAcode ,RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz.  For more information on the ViennaRNA package refer to <http://www.tbi.univie.ac.at/RNA/>.  

@@ -5,9 +5,9 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.2.6+version:             1.2.7 synopsis:            Libary for parsing ViennaRNA package output-description:         Currently contains parsers and datatypes for: RNAalifold, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz.+description:         Currently contains parsers and datatypes for: RNAalifold, RNAcode, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz. 		     . 		     For more information on the ViennaRNA package refer to <http://www.tbi.univie.ac.at/RNA/>. 		     .@@ -30,13 +30,15 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.6-  tag:      1.2.6+  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.7+  tag:      1.2.7  library   -- Modules exported by the library.   exposed-modules:   Bio.ViennaRNAParser                      Bio.ViennaRNAParserLibrary+                     Bio.RNAcodeData+                     Bio.RNAcodeParser                      Bio.RNAcofoldData                      Bio.RNAcofoldParser                      Bio.RNAfoldData@@ -56,7 +58,7 @@   ghc-options:         -Wall -O2 -fno-warn-unused-do-bind    -- Other library packages from which modules are imported.-  build-depends:       base >=4.5 && <5, parsec>=3.1.9, process+  build-depends:       base >=4.5 && <5, parsec>=3.1.9, process, transformers      -- Directories containing source files.   hs-source-dirs:      src

@@ -1,7 +1,9 @@ -*-change-log-*--+1.2.7 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 4. January 2016+	* Added RNAcode parser+	* Added stackage yaml file 1.2.6 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 7. September 2015-        * Added a options argument to RNAz systemcall function+	* Added options to RNAz syscall function 1.2.5 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 9. July 2015         * Fixed parsing of multiple warning fields and optional whitespaces in 	RNAz consensus energy

@@ -0,0 +1,35 @@+-- | This module contains a hierarchical data structure for+--   RNAcode output+--   For more information on RNAcode consult: <http://wash.github.io/rnacode/>++module Bio.RNAcodeData where+    +-- | All elements of RNAcode output are contained in this datatype +data RNAcode = RNAcode+  { +    rnacodeHits :: [RNAcodeHit],+    rcAlignmentNumber :: Maybe Int,+    rcTime :: Maybe Double,+    rcSampleNumber :: Maybe Int,+    rcDelta :: Maybe Double,+    rcBigOmega :: Maybe Double,+    rcSmallOmega :: Maybe Double,+    rcStopPenalty :: Maybe Double+  }+  deriving (Show, Eq)++-- | RNAcode Hit+data RNAcodeHit = RNAcodeHit+  { +    hss :: Int,+    frame :: Double,+    length :: Int,+    from :: Int,+    to :: Int,+    name :: String,+    start :: Int,+    end :: Int,+    score :: Double,+    pvalue :: Double+  }+  deriving (Show, Eq)

@@ -0,0 +1,112 @@+-- | Parse RNAcode output+--   For more information on RNAcode consult: <http://wash.github.io/rnacode/>+++module Bio.RNAcodeParser (+                       systemRNAcode,+                       parseRNAcode,+                       readRNAcode,+                       parseRNAcodeTabular,+                       readRNAcodeTabular,+                       module Bio.RNAcodeData+                      ) where+import Data.Functor.Identity+import Bio.RNAcodeData+import Text.ParserCombinators.Parsec+import System.Process+import System.Exit+import Text.Parsec.Token+import qualified Control.Exception.Base as CE+import Text.Parsec.Language (haskell)+import Control.Applicative ((<*>),(<$>),(<$),pure)++-- | Run external RNAcode command and read the output into the corresponding datatype+systemRNAcode :: String -> String -> String -> IO ExitCode+systemRNAcode options inputFilePath outputFilePath = system ("RNAcode " ++ options ++ " " ++ inputFilePath ++ " >" ++ outputFilePath)++-- | Parse the tabular input as RNAcode datatype+genParseRNAcodeTabular :: GenParser Char st RNAcode+genParseRNAcodeTabular = do+  _rnacodeHits <- many1 genParseRNAcodeTabularHit+  return $ RNAcode _rnacodeHits Nothing Nothing Nothing Nothing Nothing Nothing Nothing++-- | 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+  _start <- natural haskell+  _end <- natural haskell+  _score <- float haskell+  _pvalue <- float haskell+  return $ RNAcodeHit (fromInteger _hss) (fromInteger _frame) (fromInteger _length) (fromInteger _from) (fromInteger _to) _name (fromInteger _start) (fromInteger _end) _score _pvalue +++-- | Parse the input as RNAcode datatype+genParseRNAcode :: GenParser Char st RNAcode+genParseRNAcode = do+  many1 (oneOf " \n")+  string "HSS # Frame Length  From    To        Name       Start         End    Score        P"+  newline+  string "======================================================================================"+  newline+  _rnacodeHits <- many1 (try genParseRNAcodeHit)+  newline+  _alignmentnumber <- natural haskell+  string "alignment(s) scored in "+  _time <- float haskell+  string "seconds. Parameters used:"+  newline+  string "N="+  _samples <- natural haskell+  string ", Delta="+  --_delta <- float haskell+  _delta <- (try (negate <$ char '-') <|> pure id) <*> float haskell+  string ", Omega="+  _bigomega <- (try (negate <$ char '-') <|> pure id) <*> float haskell+  string ", omega="+  _smallomega <- (try (negate <$ char '-') <|> pure id) <*> float haskell+  string ", stop penalty="+  _stopPenalty <- (try (negate <$ char '-') <|> pure id) <*> float haskell+  return $ RNAcode _rnacodeHits (Just (fromInteger _alignmentnumber)) (Just _time) (Just (fromInteger _samples)) (Just _delta) (Just _bigomega) (Just _smallomega) (Just _stopPenalty)++-- | Parse the input as RNAcodeHit+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+  _start <- natural haskell+  _end <- natural haskell+  _score <- float haskell+  _pvalue <- many1 (try (choice [digit,char '.']))+  newline+  return $ RNAcodeHit (fromInteger _hss) (fromInteger _frame) (fromInteger _length) (fromInteger _from) (fromInteger _to) _name (fromInteger _start) (fromInteger _end) _score (read _pvalue :: Double)++-- | parse RNAcode from input string+parseRNAcode :: String -> Either ParseError RNAcode+parseRNAcode = parse genParseRNAcode "parseRNAcode"++-- | parse RNAcode from input filePath                      +readRNAcode :: String -> IO (Either ParseError RNAcode)                  +readRNAcode filePath = do +  parsedFile <- parseFromFile genParseRNAcode filePath+  CE.evaluate parsedFile++-- | parse RNAcode from input string+parseRNAcodeTabular :: String -> Either ParseError RNAcode+parseRNAcodeTabular = parse genParseRNAcodeTabular "parseRNAcode" ++-- | parse RNAcode from input filePath                      +readRNAcodeTabular :: String -> IO (Either ParseError RNAcode)                  +readRNAcodeTabular filePath = do +  parsedFile <- parseFromFile genParseRNAcodeTabular filePath+  CE.evaluate parsedFile

@@ -3,7 +3,9 @@ -- For more information on the Vienna RNAPackage consult: <http://www.tbi.univie.ac.at/~ivo/RNA/> -- or the homepage of the current maintainer: <http://www.tbi.univie.ac.at/~ronny/RNA/index.html> -module Bio.ViennaRNAParser ( +module Bio.ViennaRNAParser (+                       module Bio.RNAcodeData,+                       module Bio.RNAcodeParser,                        module Bio.RNAcofoldData,                        module Bio.RNAcofoldParser,                                                   module Bio.RNAplexData,@@ -19,6 +21,8 @@                        module Bio.RNAupData,                        module Bio.RNAupParser                       ) where+import Bio.RNAcodeData+import Bio.RNAcodeParser import Bio.RNAcofoldData import Bio.RNAcofoldParser import Bio.RNAplexData