ViennaRNAParser 1.0.1 → 1.2.0

raw patch · 16 files changed

+176/−38 lines, 16 filesdep +ViennaRNAParserdep +hspecdep +processdep ~basedep ~parsecPVP ok

version bump matches the API change (PVP)

Dependencies added: ViennaRNAParser, hspec, process

Dependency ranges changed: base, parsec

API changes (from Hackage documentation)

Files

• README.md +8/−0
• ViennaRNAParser.cabal +21/−9
• changelog +11/−0
• src/Bio/RNAalifoldData.hs +1/−1
• src/Bio/RNAalifoldParser.hs +17/−6
• src/Bio/RNAcofoldData.hs +14/−0
• src/Bio/RNAcofoldParser.hs +49/−0
• src/Bio/RNAfoldData.hs +3/−4
• src/Bio/RNAfoldParser.hs +12/−2
• src/Bio/RNAplexParser.hs +1/−0
• src/Bio/RNAupData.hs +1/−1
• src/Bio/RNAupParser.hs +9/−2
• src/Bio/RNAzData.hs +1/−1
• src/Bio/RNAzParser.hs +21/−11
• src/Bio/ViennaRNAParser.hs +5/−1
• test-suite/Spec.hs +2/−0

@@ -0,0 +1,8 @@+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.++For more information on the ViennaRNA package refer to <http://www.tbi.univie.ac.at/RNA/>. ++The libary is tested with Version 2.1.9 of the ViennaRNA package.

@@ -5,10 +5,13 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.0.1+version:             1.2.0 synopsis:            Libary for parsing ViennaRNA package output-description:         Currently contains parsers and datatypes for: RNAplex, RNAz. The libary is tested with Version >2.0 of the ViennaRNA package.-                     +description:         Currently contains parsers and datatypes for: RNAalifold, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz.+		     .+		     For more information on the ViennaRNA package refer to <http://www.tbi.univie.ac.at/RNA/>.+		     .+		     The libary is tested with Version 2.1.9 of the ViennaRNA package.                       license:             GPL license-file:        LICENSE author:              Florian Eggenhofer@@ -18,19 +21,24 @@ build-type:          Simple cabal-version:       >=1.8 +extra-source-files:+  README.md changelog+ source-repository head   type:     git   location: https://github.com/eggzilla/ViennaRNAParser  source-repository this   type:     git-  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.0.1-  tag:      1.0.1+  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.0+  tag:      1.2.0  library   -- Modules exported by the library.   exposed-modules:   Bio.ViennaRNAParser-  other-modules:     Bio.RNAfoldData+                     Bio.RNAcofoldData+                     Bio.RNAcofoldParser+                     Bio.RNAfoldData                      Bio.RNAfoldParser                      Bio.RNAplexData                      Bio.RNAplexParser@@ -47,9 +55,13 @@   ghc-options:         -Wall -O2 -fno-warn-unused-do-bind    -- Other library packages from which modules are imported.-  build-depends:       base >=4.5 && <5, parsec+  build-depends:       base >=4.5 && <5, parsec>=3.1.9, process      -- Directories containing source files.   hs-source-dirs:      src-  -    ++test-suite hspec+    build-depends:    base, parsec, ViennaRNAParser, hspec>=1.8+    hs-source-dirs:   test-suite+    main-is:          Spec.hs+    type:             exitcode-stdio-1.0

@@ -0,0 +1,11 @@+-*-change-log-*-+1.2.0 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 1. July 2015+	* Added Hspec test-suite+	* Added RNAcofold parser+1.1.0 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 2. June 2015+	* Exposed submodules for imports, added systemcalls for RNAalifold,+	RNAfold, RNAz+1.0.1 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 1. March 2015+	* Added Travis CI support+	* Added -Wall and -O2 compiler options+	* Added RNAfold, RNAalifold, RNAdistance, RNAup parsers

@@ -4,7 +4,7 @@ module Bio.RNAalifoldData where  -- | Data structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequence-data RNAalifoldOutput = RNAalifoldOutput+data RNAalifold = RNAalifold   {     alignmentConsensusSequence :: String,     alignmentConsensusDotBracket :: String,

@@ -2,6 +2,7 @@ --   For more information on RNAalifold consult: <>  module Bio.RNAalifoldParser (+                       systemRNAalifold,                        parseRNAalifold,                        readRNAalifold,                                                         module Bio.RNAalifoldData@@ -9,18 +10,26 @@  import Bio.RNAalifoldData import Text.ParserCombinators.Parsec+import System.Process+import System.Exit+import qualified Control.Exception.Base as CE  readDouble :: String -> Double readDouble = read               +--- | Run external RNAalifold command and read the output into the corresponding datatype+systemRNAalifold :: String -> String -> String -> IO ExitCode+systemRNAalifold options inputFilePath outputFilePath = system ("RNAalifold " ++ options  ++ " < " ++ inputFilePath  ++ " > " ++ outputFilePath)+ -- | Parse the consenus of RNAz results         -genParserRNAalifold :: GenParser Char st RNAalifoldOutput+genParserRNAalifold :: GenParser Char st RNAalifold genParserRNAalifold = do   _sequence <- many1 (noneOf "\n")                   newline   secondaryStructure <- many1 (oneOf "&().,")   string (" (")-  foldingEnergy <- many1 (noneOf " ")+  optional space+  foldingEnergy <- many1 (oneOf "-.1234567890")   string " ="   many1 space   initialFoldingEnergy <- many1 (noneOf " ")@@ -30,13 +39,15 @@   string (")")   many1 space   eof-  return $ RNAalifoldOutput _sequence secondaryStructure (readDouble foldingEnergy) (readDouble initialFoldingEnergy) (readDouble covarianceContributionEnergy)+  return $ RNAalifold _sequence secondaryStructure (readDouble foldingEnergy) (readDouble initialFoldingEnergy) (readDouble covarianceContributionEnergy)     -- | parse RNAalifold output from input string-parseRNAalifold :: [Char] -> Either ParseError RNAalifoldOutput+parseRNAalifold :: [Char] -> Either ParseError RNAalifold parseRNAalifold input = parse genParserRNAalifold "genParseRNAalifold" input  -- | parse RNAalifold output from input filePath                      -readRNAalifold :: String -> IO (Either ParseError RNAalifoldOutput)                  -readRNAalifold filePath = parseFromFile genParserRNAalifold filePath+readRNAalifold :: String -> IO (Either ParseError RNAalifold)+readRNAalifold filePath = do+  parsedFile <- parseFromFile genParserRNAalifold filePath+  CE.evaluate parsedFile 

@@ -0,0 +1,14 @@+-- | This module contains a data structure for RNAcofold output+--   For more information on RNAcofold consult: <http://www.tbi.univie.ac.at/RNA/RNAcofold.html>++module Bio.RNAcofoldData where+-- | Data structure for cofolding of 2 nucleic acid sequences+data RNAcofold = RNAcofold+  { +    coFoldSequence1 :: String,+    coFoldSequence2 :: String,+    coFoldSecondaryStructure1 :: String,+    coFoldSecondaryStructure2 :: String,+    coFoldingEnergy :: Double+  }+  deriving (Show, Eq)

@@ -0,0 +1,49 @@+-- | Parse RNAfold output+--   For more information on RNAcofold consult: <http://www.tbi.univie.ac.at/RNA/RNAcofold.html>++module Bio.RNAcofoldParser (+                       systemRNAcofold,+                       parseRNAcofold,+                       readRNAcofold,                                   +                       module Bio.RNAcofoldData+                      ) where++import Bio.RNAcofoldData+import Text.ParserCombinators.Parsec+import System.Process +import System.Exit+import qualified Control.Exception.Base as CE++-- | Run external RNAcofold command +systemRNAcofold :: String -> String -> IO ExitCode+systemRNAcofold inputFilePath outputFilePath = system ("RNAcofold  <" ++ inputFilePath  ++ " >" ++ outputFilePath)++readDouble :: String -> Double+readDouble = read              ++-- | Parse the consenus of RNAcofold results         +genParserRNAcofold :: GenParser Char st RNAcofold+genParserRNAcofold = do +  _coFoldSequence1 <- many1 (oneOf "NATUGCatugc")+  string "&"+  _coFoldSequence2 <- many1 (oneOf "NATUGCatugc")+  newline+  _coFoldSecondaryStructure1 <- many1 (oneOf "().,")+  string "&"+  _coFoldSecondaryStructure2 <- many1 (oneOf "().,")+  space+  string ("(")+  optional space+  _coFoldingEnergy <- many1 (oneOf "-1234567890.")+  string (")")+  return $ RNAcofold _coFoldSequence1 _coFoldSequence2 _coFoldSecondaryStructure1 _coFoldSecondaryStructure2 (readDouble _coFoldingEnergy)++-- | parse RNAcofold output from input string+parseRNAcofold :: [Char] -> Either ParseError RNAcofold+parseRNAcofold input = parse genParserRNAcofold "genParseRNAcofold" input++-- | parse RNAcofold output from input filePath                      +readRNAcofold :: String -> IO (Either ParseError RNAcofold)                  +readRNAcofold filePath = do+  parsedFile <- parseFromFile genParserRNAcofold filePath+  CE.evaluate parsedFile

@@ -1,9 +1,8 @@--- | This module contains a hierarchical data structure for---   RNAplex output---   For more information on RNAplex consult: <http://www.bioinf.uni-leipzig.de/Software/RNAplex/>+-- | This module contains a data structure for RNAfold output+--   For more information on RNAplex consult: <http://www.tbi.univie.ac.at/RNA/RNAfold.html>  module Bio.RNAfoldData where--- | Data structure for individual interaction between a target and query nucleic acid seqence+-- | Data structure for RNAfold data RNAfold = RNAfold   {      sequenceIdentifier :: String,

@@ -1,7 +1,8 @@ -- | Parse RNAfold output---   For more information on RNAplex consult: <>+--   For more information on RNAfold consult: <http://www.tbi.univie.ac.at/RNA/RNAfold>  module Bio.RNAfoldParser (+                       systemRNAfold,                        parseRNAfold,                        readRNAfold,                                                           module Bio.RNAfoldData@@ -9,7 +10,14 @@  import Bio.RNAfoldData import Text.ParserCombinators.Parsec+import System.Process +import System.Exit+import qualified Control.Exception.Base as CE +-- | Run external RNAfold command and read the output into the corresponding datatype+systemRNAfold :: String -> String -> IO ExitCode+systemRNAfold inputFilePath outputFilePath = system ("RNAfold --noPS  <" ++ inputFilePath  ++ " >" ++ outputFilePath)+ readDouble :: String -> Double readDouble = read               @@ -34,4 +42,6 @@  -- | parse RNAfold output from input filePath                       readRNAfold :: String -> IO (Either ParseError RNAfold)                  -readRNAfold filePath = parseFromFile genParserRNAfold filePath+readRNAfold filePath = do+  parsedFile <- parseFromFile genParserRNAfold filePath+  CE.evaluate parsedFile

@@ -46,6 +46,7 @@   _queryDuplexEnd <- many1 digit   many1 space   char '('+  optional space   _duplexEnergy <- many1 (noneOf (" )"))   optional space   optional (char '=')

@@ -28,6 +28,6 @@   upTargetAccessibility :: Maybe Double,   upQuerySequence :: String,   upTargetSequence :: String,-  upOutputFileName :: String+  upOutputFileName :: Maybe String  }  deriving (Show, Eq)

@@ -71,9 +71,16 @@   char '&'   targetSequence <- many1 (noneOf ("\n"))   newline-  _upOutputFileName <- many1 (noneOf ("\n"))-  newline+  _upOutputFileName <- optionMaybe (try parseRNAupFileName)   return $ RNAupInteractionRegion upsecondaryStructure (readInt uptargetDuplexBegin) (readInt uptargetDuplexEnd) (readInt upqueryDuplexBegin) (readInt upqueryDuplexEnd) (readDouble upduplexEnergy) (liftM readDouble upduplexEnergyWithoutAccessiblity) (liftM readDouble upqueryAccessiblity) (liftM readDouble uptargetAccessibility) querySequence targetSequence _upOutputFileName++-- | Parse a RNAupFileName+parseRNAupFileName :: GenParser Char st String+parseRNAupFileName = do+  string "RNAup output in file: "+  fileName <- many1 (noneOf ("\n>"))+  newline+  return fileName  -- | parse RNAupOutput from input string parseRNAup :: [Char] -> Either ParseError [RNAupInteraction]

@@ -6,7 +6,7 @@ --import Biobase.RNA      -- | All elements of RNAz output are contained in this datatype -data RNAzOutput = RNAzOutput+data RNAz = RNAz   { version :: String,     sequenceNumber :: Int,     columnNumber :: Int,

@@ -3,6 +3,7 @@ -- | Parse RNAz output --   For more information on RNAz consult: <http://www.tbi.univie.ac.at/~wash/RNAz module Bio.RNAzParser (+                       systemRNAz,                        parseRNAz,                        readRNAz,                                                           module Bio.RNAzData@@ -10,6 +11,9 @@  import Bio.RNAzData import Text.ParserCombinators.Parsec+import System.Process+import System.Exit+import qualified Control.Exception.Base as CE  readDouble :: String -> Double readDouble = read              @@ -17,9 +21,13 @@ readInt :: String -> Int readInt = read --- | Parse the input as RNAzOutput datatype-parseRNAzOutput :: GenParser Char st RNAzOutput-parseRNAzOutput = do+-- | Run external RNAz command and read the output into the corresponding datatype+systemRNAz :: String -> String -> IO ExitCode+systemRNAz inputFilePath outputFilePath = system ("RNAz " ++ inputFilePath ++ " >" ++ outputFilePath)++-- | Parse the input as RNAz datatype+genParseRNAz :: GenParser Char st RNAz+genParseRNAz = do   char '\n'   many1 (oneOf "# ")   string "RNAz"@@ -54,7 +62,7 @@   newline   _rnaZResults  <- many1 (try parseRNAzResult)   _rnaZConsensus <- parseRNAzConsensus         -  return $ RNAzOutput _version _sequences _columns _readingDirection _meanPairwiseIdentity _shannonEntropy _gcContent _meanSingleSequenceMFE _consensusMFE _energyContribution _covarianceContribution _combinationsPair _meanZScore _structureConservationIndex _backgroundModel _decisionModel _svmDecisionValue _svmRNAClassProbability _prediction _rnaZResults _rnaZConsensus+  return $ RNAz _version _sequences _columns _readingDirection _meanPairwiseIdentity _shannonEntropy _gcContent _meanSingleSequenceMFE _consensusMFE _energyContribution _covarianceContribution _combinationsPair _meanZScore _structureConservationIndex _backgroundModel _decisionModel _svmDecisionValue _svmRNAClassProbability _prediction _rnaZResults _rnaZConsensus  -- | Parse a RNAz field containing a Double  parseRNAzDoubleField :: String -> GenParser Char st Double@@ -92,7 +100,7 @@   _header <- many1 (noneOf "\n")   newline    notFollowedBy (string (">consensus"))-  _resultSequence <- many1 (oneOf "~-NATUGCatugc")         +  _resultSequence <- many1 (oneOf "~_-.NATUGCatugc")            newline           _dotBracket <- many1 (oneOf "-().,")   space@@ -118,7 +126,7 @@ parseRNAzConsensus = do   string (">consensus")   newline-  _consensusSequence <- many1 (oneOf "~_-NATUGCatugc")                 +  _consensusSequence <- many1 (oneOf "~_-.NATUGCatugc")                    newline             _dotBracket <- many1 (oneOf "().,")   space@@ -140,10 +148,12 @@   eof      return $ RNAzConsensus _consensusSequence _dotBracket          --- | parse RNAzOutput from input string-parseRNAz :: [Char] -> Either ParseError RNAzOutput-parseRNAz input = parse parseRNAzOutput "parseRNAzOutput" input+-- | parse RNAz from input string+parseRNAz :: [Char] -> Either ParseError RNAz+parseRNAz input = parse genParseRNAz "parseRNAz" input  -- | parse from input filePath                      -readRNAz :: String -> IO (Either ParseError RNAzOutput)                  -readRNAz filePath = parseFromFile parseRNAzOutput filePath+readRNAz :: String -> IO (Either ParseError RNAz)                  +readRNAz filePath = do +  parsedFile <- parseFromFile genParseRNAz 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.RNAcofoldData,+                       module Bio.RNAcofoldParser,                                                   module Bio.RNAplexData,                        module Bio.RNAplexParser,                        module Bio.RNAzData,@@ -17,6 +19,8 @@                        module Bio.RNAupData,                        module Bio.RNAupParser                       ) where+import Bio.RNAcofoldData+import Bio.RNAcofoldParser import Bio.RNAplexData import Bio.RNAplexParser import Bio.RNAzData

@@ -0,0 +1,2 @@+-- test-suite/Spec.hs+{-# OPTIONS_GHC -F -pgmF hspec-discover #-}