ViennaRNAParser 1.2.2 → 1.2.3

raw patch · 4 files changed

+9/−7 lines, 4 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

ViennaRNAParser.cabal +3/−3
changelog +2/−0
src/Bio/RNAzParser.hs +2/−2
src/Bio/ViennaRNAParserLibrary.hs +2/−2

ViennaRNAParser.cabal view

@@ -5,7 +5,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.2.2+version:             1.2.3 synopsis:            Libary for parsing ViennaRNA package output description:         Currently contains parsers and datatypes for: RNAalifold, RNAdistance, RNAcofold, RNAfold, RNAplex, RNAup, RNAz. 		     .@@ -30,8 +30,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.2-  tag:      1.2.2+  location: https://github.com/eggzilla/ViennaRNAParser/tree/1.2.3+  tag:      1.2.3  library   -- Modules exported by the library.

changelog view

@@ -1,4 +1,6 @@ -*-change-log-*-+1.2.3 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 7. July 2015+	* Added lower case letters to allowed sequence characters 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

src/Bio/RNAzParser.hs view

@@ -1,3 +1,4 @@+ -- | Parse RNAz output --   For more information on RNAz consult: <http://www.tbi.univie.ac.at/~wash/RNAz module Bio.RNAzParser (@@ -49,8 +50,7 @@   _svmDecisionValue <-  parseRNAzDoubleField "SVM decision value:"   _svmRNAClassProbability <- parseRNAzDoubleField "SVM RNA-class probability:"   _prediction <- parseRNAzStringField "Prediction:"-  optional (try (string " WARNING: Mean z-score out of range."))-  optional (try newline)+  _ <- optional (try (parseRNAzStringField " WARNING:"))   newline   many1 (char '#')    newline

src/Bio/ViennaRNAParserLibrary.hs view

@@ -19,13 +19,13 @@ -- | Parse nucleotide sequence. Allowed letters according to IUPAC parseNucleotideSequence :: GenParser Char st String parseNucleotideSequence = do-  nucleotideSequence <- many1 (oneOf "RYSWKMBDHVNATUGCatugc") +  nucleotideSequence <- many1 (oneOf "RYSWKMBDHVNATUGCryswkmbdhvnatugc")    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") +  entry <- many1 (oneOf "~_-.RYSWKMBDHVNATUGCryswkmbdhvnatugc")    return $ entry  -- | Parse protein amino acid code sequence. Allowed letters according to IUPAC