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eggzillaeggzilla
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Merge pull request #19 from eggzilla/globaliterationfix
Scan - Fixed empty genomes fasta in global search step
2 parents 374b5b3 + 950be6e commit 59b8a91

8 files changed

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‎.travis.yml‎

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@@ -11,11 +11,11 @@ before_script:
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script:
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- docker create --name develcontainer devel
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- mkdir RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlien/build/RNAlien/RNAlien RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlienStatistics/build/RNAlienStatistics/RNAlienStatistics RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/cmsearchToBed/build/cmsearchToBed/cmsearchToBed RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAcentralHTTPRequest/build/RNAcentralHTTPRequest/RNAcentralHTTPRequest RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlienScan/build/RNAlienScan/RNAlienScan RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlien/build/RNAlien/RNAlien RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlienStatistics/build/RNAlienStatistics/RNAlienStatistics RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/cmsearchToBed/build/cmsearchToBed/cmsearchToBed RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAcentralHTTPRequest/build/RNAcentralHTTPRequest/RNAcentralHTTPRequest RNAlien
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- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlienScan/build/RNAlienScan/RNAlienScan RNAlien
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- cp LICENSE RNAlien
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- tar -cvzf RNAlien.tar.gz RNAlien
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‎Biobase/RNAlien.hs‎

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let inputSequence = head reformatedFastaInput
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initialTaxId <- setInitialTaxId offlineMode threads inputBlastDatabase temporaryDirectoryPath inputTaxId inputSequence
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let checkedTaxonomyRestriction = checkTaxonomyRestriction taxonomyRestriction
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let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) inputTaxId singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads inputBlastDatabase checkedTaxonomyRestriction (setVerbose verboseLevel) offlineMode
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let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) inputTaxId singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads inputBlastDatabase checkedTaxonomyRestriction (setVerbose verboseLevel) offlineMode []
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let initialization = ModelConstruction iterationNumber reformatedFastaInput [] initialTaxId Nothing (fromJust inputEvalueCutoff) False [] [] []
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logMessage (show initialization) temporaryDirectoryPath
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modelConstructionResults <- modelConstructer staticOptions initialization

‎Biobase/RNAlien/Library.hs‎

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@@ -2199,10 +2199,11 @@ scanModelConstructionResult staticOptions modelConstruction = do
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createDirectoryIfMissing False logFileDirectoryPath
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let expectThreshold = setBlastExpectThreshold modelConstruction
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let (upperTaxLimit,lowerTaxLimit) = (Just (0 :: Int), Nothing)
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let currentGenomeFasta = genomeFastas modelConstruction
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let genomeFastaPath = (iterationDirectory ++ "genome.fa")
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writeFastaFile genomeFastaPath currentGenomeFasta
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candidates1 <- catchAll (searchCandidates staticOptions Nothing currentIterationNumber upperTaxLimit lowerTaxLimit expectThreshold (Just genomeFastaPath) queries)
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--let currentGenomeFasta = genomeFastas modelConstruction
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-- Genome for global search is copied from input
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let currentGenomeFastasPath = (iterationDirectory ++ "genome.fa")
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copyFile (genomeFastasPath staticOptions) currentGenomeFastasPath
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candidates1 <- catchAll (searchCandidates staticOptions Nothing currentIterationNumber upperTaxLimit lowerTaxLimit expectThreshold (Just currentGenomeFastasPath) queries)
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(\e -> do logWarning ("Warning: Search results iteration" ++ show currentIterationNumber ++ " - exception: " ++ show e) outputDirectory
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return (SearchResult [] Nothing))
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let uniqueCandidates = filterDuplicates modelConstruction candidates1

‎Biobase/RNAlien/Types.hs‎

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blastDatabase :: Maybe String,
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taxRestriction :: Maybe String,
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verbositySwitch :: Bool,
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offline :: Bool
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offline :: Bool,
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genomeFastasPath :: String
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} deriving (Show)
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-- | Keeps track of model construction

‎Biobase/RNAlienScan.hs‎

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when (null inputGenomesFasta) (error "Please provide input genomes with the cmd line parameter -s")
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logToolVersions inputQuerySelectionMethod temporaryDirectoryPath
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let reformatedFastaInput = map reformatFasta fastaInput
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let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) Nothing singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads Nothing Nothing (setVerbose verboseLevel) True
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let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) Nothing singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads Nothing Nothing (setVerbose verboseLevel) True inputGenomesFastaFilePath
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let initialization = ModelConstruction iterationNumber reformatedFastaInput [] Nothing Nothing (fromJust inputEvalueCutoff) False [] [] inputGenomesFasta
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logMessage (show initialization) temporaryDirectoryPath
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modelConstructionResults <- scanModelConstructer staticOptions initialization

‎ChangeLog.md‎

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-*-change-log-*-
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### 1.7.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) tbd
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### 1.7.1 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 12. September 2019
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* Fixed Scan tool global search step
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### 1.7.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 29. August 2019
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* Added Scan tool
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* Changed tracing high similarity candidates

‎README.md‎

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RNAlien is available with all dependencies via [biocontainer](https://quay.io/repository/biocontainers/rnalien). Install
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[docker](https://www.docker.com/get-docker)
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docker pull quay.io/biocontainers/rnalien:1.7.0--pl5.22.0_0
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docker run -i -t quay.io/biocontainers/rnalien:1.7.0--pl5.22.0_0 bash
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docker pull quay.io/biocontainers/rnalien:1.7.1--pl5.22.0_0
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docker run -i -t quay.io/biocontainers/rnalien:1.7.1--pl5.22.0_0 bash
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### <u>Installation via cabal-install</u>
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‎RNAlien.cabal‎

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name: RNAlien
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version: 1.7.0
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version: 1.7.1
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synopsis: Unsupervized construction of RNA family models
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description: RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.
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.
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source-repository this
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type: git
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location: https://github.com/eggzilla/RNAlien/tree/1.7.0
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tag: 1.7.0
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location: https://github.com/eggzilla/RNAlien/tree/1.7.1
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tag: 1.7.1
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executable RNAlien
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Hs-Source-Dirs: ./Biobase/

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