diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ The source code of *cmv* is open source and available via GitHub and Hackage (License GPL-3): -* [![GitHub](https://img.shields.io/github/tag/eggzilla/cmv.svg)](https://github.com/eggzilla/cmv) [![Build Status](https://travis-ci.org/eggzilla/cmv.svg?branch=master)](https://travis-ci.org/eggzilla/cmv) [![Hackage](https://img.shields.io/hackage/v/cmv.svg)](https://hackage.haskell.org/package/cmv) [![Bioconda](https://anaconda.org/bioconda/cmv/badges/version.svg)](https://anaconda.org/bioconda/cmv) [![Docker Repository on Quay](https://quay.io/repository/biocontainers/cmv/status "Docker Repository on Quay")](https://quay.io/repository/repository/biocontainers/cmv) +* [![GitHub](https://img.shields.io/github/tag/eggzilla/cmv.svg)](https://github.com/eggzilla/cmv) [![Build Status](https://travis-ci.org/eggzilla/cmv.svg?branch=master)](https://travis-ci.org/eggzilla/cmv) [![Hackage](https://img.shields.io/hackage/v/cmv.svg)](https://hackage.haskell.org/package/cmv) [![Bioconda](https://anaconda.org/bioconda/cmv/badges/version.svg)](https://anaconda.org/bioconda/cmv) [![Docker Repository on Quay](https://quay.io/repository/biocontainers/cmv/status "Docker Repository on Quay")](https://quay.io/repository/biocontainers/cmv) For instruction how to use *cmv* please see the [Help page.](http://www.gapjunction.eu/cmvs/help) diff --git a/changelog b/changelog --- a/changelog +++ b/changelog @@ -1,4 +1,7 @@ -*-change-log-*- +1.0.8 Florian Eggenhofer 27. January 2018 + * Fixed secondary structure visualisation for missing consensus + secondary structure 1.0.7 Florian Eggenhofer 15. January 2018 * Improved placment of index labels * Prepared for layout direction extension diff --git a/cmv.cabal b/cmv.cabal --- a/cmv.cabal +++ b/cmv.cabal @@ -1,5 +1,5 @@ name: cmv -version: 1.0.7 +version: 1.0.8 synopsis: Detailed visualization of CMs, HMMs and their comparisions description: cmv is a collection of tools for the visualisation of Hidden Markov Models (HMMV) and RNA-family models (CMV). Moreover it can visualise comparisons of these models (HMMCV,CMCV), and annotate linked regions in the structural alignments they were constructed from and via, 3rd party tools, in their consensus secondary structure. license: GPL-3 @@ -20,8 +20,8 @@ source-repository this type: git - location: https://github.com/eggzilla/cmv/tree/1.0.7 - tag: 1.0.7 + location: https://github.com/eggzilla/cmv/tree/1.0.8 + tag: 1.0.8 library -- Modules exported by the library. diff --git a/src/Bio/CMDraw.hs b/src/Bio/CMDraw.hs --- a/src/Bio/CMDraw.hs +++ b/src/Bio/CMDraw.hs @@ -192,7 +192,8 @@ r2rInputPrefix = sHeader ++ sConsensusStructure ++ sConsensusSequence ++ sConsensusSequenceColor ++ sCovarianceAnnotation allColumnAnnotations = columnAnnotations aln consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations) - consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList) + firstSeq = T.unpack (entrySequence (head (sequenceEntries aln))) + consensusSequence = if null consensusSequenceList then firstSeq else T.unpack (head consensusSequenceList) gapFreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence) consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations) consensusStructure = if null consensusStructureList then "" else T.unpack (head consensusStructureList) @@ -240,7 +241,8 @@ fornaInput = (fornaFilePath,fornaString) allColumnAnnotations = columnAnnotations aln consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations) - consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList) + firstSeq = T.unpack (entrySequence (head (sequenceEntries aln))) + consensusSequence = if null consensusSequenceList then firstSeq else T.unpack (head consensusSequenceList) gapfreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence) consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations) consensusStructure = if null consensusStructureList then "" else T.unpack (head consensusStructureList) @@ -267,7 +269,8 @@ fornaFilePath = structureFilePath ++ modelName ++ ".fornalink" allColumnAnnotations = columnAnnotations aln consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations) - consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList) + firstSeq = T.unpack (entrySequence (head (sequenceEntries aln))) + consensusSequence = if null consensusSequenceList then firstSeq else T.unpack (head consensusSequenceList) gapfreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence) modelName = T.unpack (CM._name inputCM) consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations) @@ -327,7 +330,8 @@ fornaInput = ">" ++ modelName ++ "\n" ++ gapfreeConsensusSequence ++ "\n" ++ gapFreeConsensusStructure allColumnAnnotations = columnAnnotations aln consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations) - consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList) + firstSeq = T.unpack (entrySequence (head (sequenceEntries aln))) + consensusSequence = if null consensusSequenceList then firstSeq else T.unpack (head consensusSequenceList) gapfreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence) modelName = T.unpack (CM._name inputCM) consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations) @@ -356,7 +360,8 @@ r2rInput = sHeader ++ sConsensusStructure ++ sConsensusSequence ++ sConsensusSequenceColor ++ sCovarianceAnnotation ++ sComparisonHighlight ++ sBackboneColorLabel allColumnAnnotations = columnAnnotations aln consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations) - consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList) + firstSeq = T.unpack (entrySequence (head (sequenceEntries aln))) + consensusSequence = if null consensusSequenceList then firstSeq else T.unpack (head consensusSequenceList) gapFreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence) consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations) consensusStructure = if null consensusStructureList then "" else T.unpack (head consensusStructureList) diff --git a/src/cmv/CMVisualisation.hs b/src/cmv/CMVisualisation.hs --- a/src/cmv/CMVisualisation.hs +++ b/src/cmv/CMVisualisation.hs @@ -73,7 +73,7 @@ Control.Monad.when (isLeft alnInput) $ print (fromLeft alnInput) --let outputName = diagramName "cmv" outputFormat let modelNumber = length cms - let layoutDirection = "vertical" + let layoutDirection = "vertical" let alns = if isRight alnInput then map (\a -> Just a) (fromRight alnInput) else replicate modelNumber Nothing let currentModelNames = map (T.unpack . CM._name) cms currentWD <- getCurrentDirectory