Skip to content

Commit 59b8a91

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

File tree

8 files changed

+24
-18
lines changed

8 files changed

+24
-18
lines changed

‎.travis.yml

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -11,11 +11,11 @@ before_script:
1111
script:
1212
- docker create --name develcontainer devel
1313
- mkdir RNAlien
14-
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlien/build/RNAlien/RNAlien RNAlien
15-
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlienStatistics/build/RNAlienStatistics/RNAlienStatistics RNAlien
16-
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/cmsearchToBed/build/cmsearchToBed/cmsearchToBed RNAlien
17-
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAcentralHTTPRequest/build/RNAcentralHTTPRequest/RNAcentralHTTPRequest RNAlien
18-
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.0/x/RNAlienScan/build/RNAlienScan/RNAlienScan RNAlien
14+
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlien/build/RNAlien/RNAlien RNAlien
15+
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlienStatistics/build/RNAlienStatistics/RNAlienStatistics RNAlien
16+
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/cmsearchToBed/build/cmsearchToBed/cmsearchToBed RNAlien
17+
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAcentralHTTPRequest/build/RNAcentralHTTPRequest/RNAcentralHTTPRequest RNAlien
18+
- docker cp develcontainer:/source/dist-newstyle/build/x86_64-linux/ghc-8.4.3/RNAlien-1.7.1/x/RNAlienScan/build/RNAlienScan/RNAlienScan RNAlien
1919
- cp LICENSE RNAlien
2020
- tar -cvzf RNAlien.tar.gz RNAlien
2121

‎Biobase/RNAlien.hs

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -112,7 +112,7 @@ main = do
112112
let inputSequence = head reformatedFastaInput
113113
initialTaxId <- setInitialTaxId offlineMode threads inputBlastDatabase temporaryDirectoryPath inputTaxId inputSequence
114114
let checkedTaxonomyRestriction = checkTaxonomyRestriction taxonomyRestriction
115-
let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) inputTaxId singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads inputBlastDatabase checkedTaxonomyRestriction (setVerbose verboseLevel) offlineMode
115+
let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) inputTaxId singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads inputBlastDatabase checkedTaxonomyRestriction (setVerbose verboseLevel) offlineMode []
116116
let initialization = ModelConstruction iterationNumber reformatedFastaInput [] initialTaxId Nothing (fromJust inputEvalueCutoff) False [] [] []
117117
logMessage (show initialization) temporaryDirectoryPath
118118
modelConstructionResults <- modelConstructer staticOptions initialization

‎Biobase/RNAlien/Library.hs

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -2199,10 +2199,11 @@ scanModelConstructionResult staticOptions modelConstruction = do
21992199
createDirectoryIfMissing False logFileDirectoryPath
22002200
let expectThreshold = setBlastExpectThreshold modelConstruction
22012201
let (upperTaxLimit,lowerTaxLimit) = (Just (0 :: Int), Nothing)
2202-
let currentGenomeFasta = genomeFastas modelConstruction
2203-
let genomeFastaPath = (iterationDirectory ++ "genome.fa")
2204-
writeFastaFile genomeFastaPath currentGenomeFasta
2205-
candidates1 <- catchAll (searchCandidates staticOptions Nothing currentIterationNumber upperTaxLimit lowerTaxLimit expectThreshold (Just genomeFastaPath) queries)
2202+
--let currentGenomeFasta = genomeFastas modelConstruction
2203+
-- Genome for global search is copied from input
2204+
let currentGenomeFastasPath = (iterationDirectory ++ "genome.fa")
2205+
copyFile (genomeFastasPath staticOptions) currentGenomeFastasPath
2206+
candidates1 <- catchAll (searchCandidates staticOptions Nothing currentIterationNumber upperTaxLimit lowerTaxLimit expectThreshold (Just currentGenomeFastasPath) queries)
22062207
(\e -> do logWarning ("Warning: Search results iteration" ++ show currentIterationNumber ++ " - exception: " ++ show e) outputDirectory
22072208
return (SearchResult [] Nothing))
22082209
let uniqueCandidates = filterDuplicates modelConstruction candidates1

‎Biobase/RNAlien/Types.hs

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,8 @@ data StaticOptions = StaticOptions
2323
blastDatabase :: Maybe String,
2424
taxRestriction :: Maybe String,
2525
verbositySwitch :: Bool,
26-
offline :: Bool
26+
offline :: Bool,
27+
genomeFastasPath :: String
2728
} deriving (Show)
2829

2930
-- | Keeps track of model construction

‎Biobase/RNAlienScan.hs

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -106,7 +106,7 @@ main = do
106106
when (null inputGenomesFasta) (error "Please provide input genomes with the cmd line parameter -s")
107107
logToolVersions inputQuerySelectionMethod temporaryDirectoryPath
108108
let reformatedFastaInput = map reformatFasta fastaInput
109-
let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) Nothing singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads Nothing Nothing (setVerbose verboseLevel) True
109+
let staticOptions = StaticOptions temporaryDirectoryPath sessionId (fromJust inputnSCICutoff) Nothing singleHitperTax inputQuerySelectionMethod inputQueryNumber lengthFilter coverageFilter blastSoftmasking threads Nothing Nothing (setVerbose verboseLevel) True inputGenomesFastaFilePath
110110
let initialization = ModelConstruction iterationNumber reformatedFastaInput [] Nothing Nothing (fromJust inputEvalueCutoff) False [] [] inputGenomesFasta
111111
logMessage (show initialization) temporaryDirectoryPath
112112
modelConstructionResults <- scanModelConstructer staticOptions initialization

‎ChangeLog.md

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,10 @@
11
-*-change-log-*-
22

3-
### 1.7.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) tbd
3+
### 1.7.1 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 12. September 2019
4+
5+
* Fixed Scan tool global search step
6+
7+
### 1.7.0 [Florian Eggenhofer](mailto:egg@cs.uni-freiburg.de) 29. August 2019
48

59
* Added Scan tool
610
* Changed tracing high similarity candidates

‎README.md

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,8 +48,8 @@ TaxonomyTools which can be used to visualise the organisms included in a RNAlien
4848
RNAlien is available with all dependencies via [biocontainer](https://quay.io/repository/biocontainers/rnalien). Install
4949
[docker](https://www.docker.com/get-docker)
5050

51-
docker pull quay.io/biocontainers/rnalien:1.7.0--pl5.22.0_0
52-
docker run -i -t quay.io/biocontainers/rnalien:1.7.0--pl5.22.0_0 bash
51+
docker pull quay.io/biocontainers/rnalien:1.7.1--pl5.22.0_0
52+
docker run -i -t quay.io/biocontainers/rnalien:1.7.1--pl5.22.0_0 bash
5353

5454
### <u>Installation via cabal-install</u>
5555

‎RNAlien.cabal

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
name: RNAlien
2-
version: 1.7.0
2+
version: 1.7.1
33
synopsis: Unsupervized construction of RNA family models
44
description: RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.
55
.
@@ -51,8 +51,8 @@ source-repository head
5151

5252
source-repository this
5353
type: git
54-
location: https://github.com/eggzilla/RNAlien/tree/1.7.0
55-
tag: 1.7.0
54+
location: https://github.com/eggzilla/RNAlien/tree/1.7.1
55+
tag: 1.7.1
5656

5757
executable RNAlien
5858
Hs-Source-Dirs: ./Biobase/

0 commit comments

Comments
 (0)