SelectSequencesFromMSA 1.0.3 → 1.0.4

raw patch · 3 files changed

+16/−15 lines, 3 filesdep ~ClustalParserPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: ClustalParser

API changes (from Hackage documentation)

Files

• SelectSequencesFromMSA.cabal +12/−11
• src/Bio/SelectSequences.hs +3/−4
• src/Bio/SelectSequencesLibrary.hs +1/−0

@@ -1,23 +1,24 @@ name:                SelectSequencesFromMSA-version:             1.0.3-synopsis:            SelectSequences is a tool for selection of a represenative subset of sequences from a multiple sequence alignment in clustal format.-description:         SelectSequences is a tool for selection of a represenative subset of sequences from a multiple sequence alignment in clustal format.+version:             1.0.4+synopsis:            Selects a representative subset of sequences from multiple sequence alignment.+description:         SelectSequences is a tool for selection of a representative subset of sequences from a multiple sequence alignment in clustal format.                      .                      Optional Dependencies:-		     .-		     * <https://www.tbi.univie.ac.at/~wash/RNAz/ RNAz>-+                     .+                     * <https://www.tbi.univie.ac.at/~wash/RNAz/ RNAz>+                                           Installation via cabal-install:                      .                      > cabal install SelectSequencesFromMSA-		     + license:             GPL-3 license-file:        LICENSE author:              Florian Eggenhofer-maintainer:          egg@tbi.univie.ac.at         +maintainer:          egg@informatik.uni.freiburg.de category:            Bioinformatics build-type:          Simple cabal-version:       >=1.8+Tested-With: GHC == 7.10.3, GHC == 8.2.2  source-repository head   type:     git@@ -25,8 +26,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/SelectSequencesFromMSA/tree/1.0.3-  tag:      1.0.3+  location: https://github.com/eggzilla/SelectSequencesFromMSA/tree/1.0.4+  tag:      1.0.4                       executable SelectSequencesFromMSA   Hs-Source-Dirs:      ./src/Bio/@@ -37,5 +38,5 @@ Library   Hs-Source-Dirs:      ./src/   ghc-options:         -Wall -fno-warn-unused-do-bind-  build-depends:       base >=4.5 && <5, cmdargs, ViennaRNAParser>=1.3.2, process, directory, biofasta, parsec, biocore, bytestring, either-unwrap, containers, ClustalParser>=1.2.1, vector, matrix, filepath, text, transformers, text-metrics+  build-depends:       base >=4.5 && <5, cmdargs, ViennaRNAParser>=1.3.2, process, directory, biofasta, parsec, biocore, bytestring, either-unwrap, containers, ClustalParser>=1.2.2, vector, matrix, filepath, text, transformers, text-metrics   Exposed-Modules:     Bio.SelectSequencesLibrary

@@ -33,19 +33,19 @@     referenceSequence = True &= name "x" &= help "The first sequence (=reference sequence) is always present in the output alignment per default. Default: True",     distanceMatrixPath = "" &= name "d" &= help "Path to distance matrix output file, only internal for interal sequence selection, e.g. /home/user/distmat (Default: )",     reformatIdOption = "RNAcode" &= name "r" &= help "Defines how sequence id is reformated, e.g. fitting for RNAcode or not (Default: RNAcode)"-  } &= summary "SelectSequences" &= help "Florian Eggenhofer 2016" &= verbosity+  } &= summary "SelectSequences" &= help "Florian Eggenhofer 2016-2018" &= verbosity  main :: IO () main = do   Options{..} <- cmdArgs options   currentWorkDirectory <- getCurrentDirectory-  let selectedOutputPath = if null outputPath then currentWorkDirectory else outputPath +  let selectedOutputPath = if null outputPath then currentWorkDirectory else outputPath   if toogleExternalSelectSequences     then do       resultStatus <- preprocessClustalForRNAzExternal inputClustalPath (selectedOutputPath ++ "/") seqenceNumber (truncate optimalIdentity) (truncate maximalIdenity) referenceSequence       if isRight resultStatus         then do-          let (idMatrix,resultAln) = fromRight resultStatus+          let (idMatrix,_) = fromRight resultStatus           return ()           Control.Monad.unless (null distanceMatrixPath) (writeFile distanceMatrixPath idMatrix)         else print ("A problem occured selecting sequences: " ++ fromLeft resultStatus)@@ -53,6 +53,5 @@       resultStatus <- preprocessClustalForRNAz inputClustalPath (selectedOutputPath ++ "/") seqenceNumber optimalIdentity maximalIdenity referenceSequence reformatIdOption       if isRight resultStatus         then do-          let (_,resultAln) = fromRight resultStatus           return ()         else print ("A problem occured selecting sequences: " ++ fromLeft resultStatus)

@@ -75,6 +75,7 @@   clustalText <- TI.readFile clustalFilepath   let clustalTextLines = T.lines clustalText   parsedClustalInput <- readClustalAlignment clustalFilepath+  print parsedClustalInput   let selectedClustalpath = outputPath ++ "result.selected"   if length clustalTextLines > 5     then