Merge pull request #19 from eggzilla/globaliterationfix

Scan - Fixed empty genomes fasta in global search step
eggzilla · Sep 12, 2019 · 59b8a91 · 59b8a91
2 parents 374b5b3 + 950be6e
commit 59b8a91
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Showing 8 changed files with 24 additions and 18 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -11,11 +11,11 @@ before_script:
 script:
   - docker create --name develcontainer devel
   - mkdir RNAlien
-  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlien/build/RNAlien/RNAlien RNAlien
-  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlienStatistics/build/RNAlienStatistics/RNAlienStatistics RNAlien
-  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/cmsearchToBed/build/cmsearchToBed/cmsearchToBed RNAlien
-  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAcentralHTTPRequest/build/RNAcentralHTTPRequest/RNAcentralHTTPRequest RNAlien
-  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlienScan/build/RNAlienScan/RNAlienScan RNAlien
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlien/build/RNAlien/RNAlien RNAlien
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlienStatistics/build/RNAlienStatistics/RNAlienStatistics RNAlien
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/cmsearchToBed/build/cmsearchToBed/cmsearchToBed RNAlien
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAcentralHTTPRequest/build/RNAcentralHTTPRequest/RNAcentralHTTPRequest RNAlien
+  - docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlienScan/build/RNAlienScan/RNAlienScan RNAlien
   - cp LICENSE RNAlien
   - tar -cvzf RNAlien.tar.gz RNAlien
 

diff --git a/Biobase/RNAlien.hs b/Biobase/RNAlien.hs
@@ -112,7 +112,7 @@ main = do
                    let inputSequence = head reformatedFastaInput
                    initialTaxId <- setInitialTaxId offlineMode threads inputBlastDatabase temporaryDirectoryPath inputTaxId inputSequence
                    let checkedTaxonomyRestriction = checkTaxonomyRestriction taxonomyRestriction
-                   let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) inputTaxId singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads inputBlastDatabase checkedTaxonomyRestriction (setVerbose verboseLevel) offlineMode
+                   let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) inputTaxId singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads inputBlastDatabase checkedTaxonomyRestriction (setVerbose verboseLevel) offlineMode []
                    let initialization = ModelConstruction iterationNumber reformatedFastaInput [] initialTaxId Nothing (fromJust inputEvalueCutoff) False [] [] []
                    logMessage (show initialization) temporaryDirectoryPath
                    modelConstructionResults <- modelConstructer staticOptions initialization

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

diff --git a/Biobase/RNAlien/Types.hs b/Biobase/RNAlien/Types.hs
@@ -23,7 +23,8 @@ data StaticOptions = StaticOptions
     blastDatabase :: Maybe String,
     taxRestriction :: Maybe String,
     verbositySwitch :: Bool,
-    offline :: Bool
+    offline :: Bool,
+    genomeFastasPath :: String
   } deriving (Show)
 
 -- | Keeps track of model construction

diff --git a/Biobase/RNAlienScan.hs b/Biobase/RNAlienScan.hs
@@ -106,7 +106,7 @@ main = do
                    when (null inputGenomesFasta) (error "Please provide input genomes with the cmd line parameter -s")
                    logToolVersions inputQuerySelectionMethod temporaryDirectoryPath
                    let reformatedFastaInput = map reformatFasta fastaInput
-                   let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) Nothing singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads Nothing Nothing (setVerbose verboseLevel) True
+                   let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) Nothing singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads Nothing Nothing (setVerbose verboseLevel) True inputGenomesFastaFilePath
                    let initialization = ModelConstruction iterationNumber reformatedFastaInput [] Nothing Nothing (fromJust inputEvalueCutoff) False [] [] inputGenomesFasta
                    logMessage (show initialization) temporaryDirectoryPath
                    modelConstructionResults <- scanModelConstructer staticOptions initialization

diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,6 +1,10 @@
 -*-change-log-*-
 
-### 1.7.0 [Florian Eggenhofer](mailto:[email protected]) tbd
+### 1.7.1  [Florian Eggenhofer](mailto:[email protected]) 12. September 2019
+
+	* Fixed Scan tool global search step
+
+### 1.7.0 [Florian Eggenhofer](mailto:[email protected]) 29. August 2019
 
 	* Added Scan tool
 	* Changed tracing high similarity candidates

diff --git a/README.md b/README.md
@@ -48,8 +48,8 @@ TaxonomyTools which can be used to visualise the organisms included in a RNAlien
      RNAlien is available with all dependencies via [biocontainer](https://quay.io/repository/biocontainers/rnalien). Install
      [docker](https://www.docker.com/get-docker)
 
-         docker pull quay.io/biocontainers/rnalien:1.7.0--pl5.22.0_0
-         docker run -i -t quay.io/biocontainers/rnalien:1.7.0--pl5.22.0_0 bash
+         docker pull quay.io/biocontainers/rnalien:1.7.1--pl5.22.0_0
+         docker run -i -t quay.io/biocontainers/rnalien:1.7.1--pl5.22.0_0 bash
 
     ### <u>Installation via cabal-install</u>
 

diff --git a/RNAlien.cabal b/RNAlien.cabal
@@ -1,5 +1,5 @@
 name:                RNAlien
-version:             1.7.0
+version:             1.7.1
 synopsis:            Unsupervized construction of RNA family models
 description:         RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.
                      .
@@ -51,8 +51,8 @@ source-repository head
 
 source-repository this
   type:     git
-  location: https://github.com/eggzilla/RNAlien/tree/1.7.0
-  tag:      1.7.0
+  location: https://github.com/eggzilla/RNAlien/tree/1.7.1
+  tag:      1.7.1
 
 executable RNAlien
   Hs-Source-Dirs:      ./Biobase/