diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
ViennaRNAParser [](https://hackage.haskell.org/package/ViennaRNAParser) [](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 .
diff --git a/ViennaRNAParser.cabal b/ViennaRNAParser.cabal
--- a/ViennaRNAParser.cabal
+++ b/ViennaRNAParser.cabal
@@ -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 .
.
@@ -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
diff --git a/changelog b/changelog
--- a/changelog
+++ b/changelog
@@ -1,7 +1,9 @@
-*-change-log-*-
-
+1.2.7 Florian Eggenhofer 4. January 2016
+ * Added RNAcode parser
+ * Added stackage yaml file
1.2.6 Florian Eggenhofer 7. September 2015
- * Added a options argument to RNAz systemcall function
+ * Added options to RNAz syscall function
1.2.5 Florian Eggenhofer 9. July 2015
* Fixed parsing of multiple warning fields and optional whitespaces in
RNAz consensus energy
diff --git a/src/Bio/RNAcodeData.hs b/src/Bio/RNAcodeData.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/RNAcodeData.hs
@@ -0,0 +1,35 @@
+-- | This module contains a hierarchical data structure for
+-- RNAcode output
+-- For more information on RNAcode consult:
+
+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)
diff --git a/src/Bio/RNAcodeParser.hs b/src/Bio/RNAcodeParser.hs
new file mode 100644
--- /dev/null
+++ b/src/Bio/RNAcodeParser.hs
@@ -0,0 +1,112 @@
+-- | Parse RNAcode output
+-- For more information on RNAcode consult:
+
+
+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
diff --git a/src/Bio/ViennaRNAParser.hs b/src/Bio/ViennaRNAParser.hs
--- a/src/Bio/ViennaRNAParser.hs
+++ b/src/Bio/ViennaRNAParser.hs
@@ -3,7 +3,9 @@
-- For more information on the Vienna RNAPackage consult:
-- or the homepage of the current maintainer:
-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