ViennaRNAParser 1.2.1 → 1.2.2

raw patch · 10 files changed

+60/−39 lines, 10 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ViennaRNAParser.cabal +4/−3
• changelog +4/−0
• src/Bio/RNAalifoldParser.hs +2/−4
• src/Bio/RNAcofoldParser.hs +1/−3
• src/Bio/RNAdistanceParser.hs +2/−4
• src/Bio/RNAfoldParser.hs +1/−3
• src/Bio/RNAplexParser.hs +1/−6
• src/Bio/RNAupParser.hs +1/−6
• src/Bio/RNAzParser.hs +3/−10
• src/Bio/ViennaRNAParserLibrary.hs +41/−0

@@ -5,7 +5,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.2.1+version:             1.2.2 synopsis:            Libary for parsing ViennaRNA package output description:         Currently contains parsers and datatypes for: RNAalifold, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz. 		     .@@ -30,12 +30,13 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.1-  tag:      1.2.1+  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.2+  tag:      1.2.2  library   -- Modules exported by the library.   exposed-modules:   Bio.ViennaRNAParser+                     Bio.ViennaRNAParserLibrary                      Bio.RNAcofoldData                      Bio.RNAcofoldParser                      Bio.RNAfoldData

@@ -1,4 +1,8 @@ -*-change-log-*-+1.2.2 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 4. July 2015+        * Added a new module for shared functions between modules+	* Sequence and alignment entry parsing is now in line with IUPAC+	letter code 1.2.1 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 3. July 2015         * Included parsing of warning field in RNAz output 1.2.0 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 1. July 2015

@@ -1,5 +1,5 @@ -- | Parse RNAalifold output---   For more information on RNAalifold consult: <>+--   For more information on RNAalifold consult: <<http://www.tbi.univie.ac.at/RNA/RNAalifold.html>  module Bio.RNAalifoldParser (                        systemRNAalifold,@@ -9,13 +9,11 @@                       ) where  import Bio.RNAalifoldData+import Bio.ViennaRNAParserLibrary 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

@@ -9,6 +9,7 @@                       ) where  import Bio.RNAcofoldData+import Bio.ViennaRNAParserLibrary import Text.ParserCombinators.Parsec import System.Process  import System.Exit@@ -17,9 +18,6 @@ -- | 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

@@ -1,5 +1,5 @@ -- | Parse RNAdistance output---   For more information on RNAdistance consult: <>+--   For more information on RNAdistance consult: <<http://www.tbi.univie.ac.at/RNA/RNAdistance.html>  module Bio.RNAdistanceParser (                        parseRNAdistance,@@ -8,10 +8,8 @@                       ) where  import Bio.RNAdistanceData+import Bio.ViennaRNAParserLibrary import Text.ParserCombinators.Parsec     --readInt :: String -> Int-readInt = read  -- | Parse the consenus of RNAz results          genParserRNAdistance :: GenParser Char st RNAdistance

@@ -10,6 +10,7 @@  import Bio.RNAfoldData import Text.ParserCombinators.Parsec+import Bio.ViennaRNAParserLibrary import System.Process  import System.Exit import qualified Control.Exception.Base as CE@@ -17,9 +18,6 @@ -- | 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                -- | Parse the consenus of RNAz results          genParserRNAfold :: GenParser Char st RNAfold

@@ -8,14 +8,9 @@                       ) where  import Bio.RNAplexData+import Bio.ViennaRNAParserLibrary import Text.ParserCombinators.Parsec     import Control.Monad--readDouble :: String -> Double-readDouble = read              --readInt :: String -> Int-readInt = read  -- | Parse the input as list of RNAplexInteraction datatype parseRNAplexOutput :: GenParser Char st [RNAplexInteraction]

@@ -8,14 +8,9 @@                       ) where  import Bio.RNAupData+import Bio.ViennaRNAParserLibrary import Text.ParserCombinators.Parsec     import Control.Monad--readDouble :: String -> Double-readDouble = read              --readInt :: String -> Int-readInt = read  -- | Parse the input as list of RNAupInteraction datatype parseRNAupOutput :: GenParser Char st [RNAupInteraction]

@@ -1,5 +1,3 @@-{-# LANGUAGE Arrows #-}- -- | Parse RNAz output --   For more information on RNAz consult: <http://www.tbi.univie.ac.at/~wash/RNAz module Bio.RNAzParser (@@ -10,17 +8,12 @@                       ) where  import Bio.RNAzData+import Bio.ViennaRNAParserLibrary import Text.ParserCombinators.Parsec import System.Process import System.Exit import qualified Control.Exception.Base as CE -readDouble :: String -> Double-readDouble = read              --readInt :: String -> Int-readInt = read- -- | Run external RNAz command and read the output into the corresponding datatype systemRNAz :: String -> String -> IO ExitCode systemRNAz inputFilePath outputFilePath = system ("RNAz " ++ inputFilePath ++ " >" ++ outputFilePath)@@ -102,7 +95,7 @@   _header <- many1 (noneOf "\n")   newline    notFollowedBy (string (">consensus"))-  _resultSequence <- many1 (oneOf "~_-.NATUGCatugc")         +  _resultSequence <- parseNucleotideAlignmentEntry   newline           _dotBracket <- many1 (oneOf "-().,")   space@@ -128,7 +121,7 @@ parseRNAzConsensus = do   string (">consensus")   newline-  _consensusSequence <- many1 (oneOf "~_-.NATUGCatugc")                 +  _consensusSequence <- parseNucleotideAlignmentEntry   newline             _dotBracket <- many1 (oneOf "().,")   space

@@ -0,0 +1,41 @@+-- | Library with auxiliary functions needed in multiple other modules.+module Bio.ViennaRNAParserLibrary (+                      parseNucleotideSequence,+                      parseNucleotideAlignmentEntry,+                      parseProteinSequence,+                      parseProteinAlignmentEntry,+                      readInt,+                      readDouble+                      ) where++import Text.ParserCombinators.Parsec++readDouble :: String -> Double+readDouble = read              ++readInt :: String -> Int+readInt = read++-- | Parse nucleotide sequence. Allowed letters according to IUPAC+parseNucleotideSequence :: GenParser Char st String+parseNucleotideSequence = do+  nucleotideSequence <- many1 (oneOf "RYSWKMBDHVNATUGCatugc") +  return $ nucleotideSequence++-- | Parse nucleotide alignment entry. Allowed letters according to IUPAC and commonly used gap characters+parseNucleotideAlignmentEntry :: GenParser Char st String+parseNucleotideAlignmentEntry = do+  entry <- many1 (oneOf "~_-.RYSWKMBDHVNATUGCatugc") +  return $ entry++-- | Parse protein amino acid code sequence. Allowed letters according to IUPAC+parseProteinSequence :: GenParser Char st String+parseProteinSequence = do+  proteinSequence <- many1 (oneOf "ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz") +  return $ proteinSequence++-- | Parse protein amino acid code alignment entry. Allowed letters according to IUPAC and commonly used gap characters+parseProteinAlignmentEntry :: GenParser Char st String+parseProteinAlignmentEntry = do+  entry <- many1 (oneOf "~_-.ABCDEFGHIKLMNPQRSTVWXYZabcdefghiklmnpqrstvwxyz") +  return $ entry