Merge pull request #200 from BackofenLab/dev

v2.3.2

Author: martin-raden

.github/workflows/build.yml

@@ -19,7 +19,7 @@ jobs:
     - name: Create conda environement
       run: |
         source `conda info --base`/etc/profile.d/conda.sh
-        conda create -q -n build-IntaRNA -c conda-forge -c bioconda gcc_linux-64 gxx_linux-64 boost-cpp libboost viennarna>=2.4.14 pkgconfig
+        conda create -q -n build-IntaRNA -c conda-forge -c bioconda gcc_linux-64 gxx_linux-64 boost-cpp viennarna>=2.4.14 pkgconfig
         conda activate build-IntaRNA
     - name: Script
       run: |
@@ -28,11 +28,19 @@ jobs:
         # generate autotools's files 
         bash autotools-init.sh 
         # run configure (without boost checks)
-        ./configure --prefix=$HOME/IntaRNA --with-vrna=`conda info --base`/envs/build-IntaRNA --with-boost=no --without-zlib
+        ENVPREFIX=`conda info --base`/envs/build-IntaRNA
+        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ENVPREFIX/lib
+        ./configure \
+           --prefix=$HOME/IntaRNA \
+           --with-vrna=$ENVPREFIX \
+           --with-boost=$ENVPREFIX \
+           --with-boost-libdir=$ENVPREFIX/lib \
+           --with-zlib=$ENVPREFIX
         # compile documentation
         # - make doxygen-doc
         # compile, test and install IntaRNA
-        make -j 2 && make tests -j 2 && make install
+        make -j 2 && make install
+        make tests -j 2
         ##### check IntaRNA build #####
         # run installed IntaRNA with help output
         $HOME/IntaRNA/bin/IntaRNA -h

ChangeLog

@@ -10,11 +10,60 @@
 # changes in development version since last release 
 ################################################################################
 
+
+################################################################################
+### version 3.2.2
+################################################################################  
+
 # IntaRNA
+- BUGFIX: maximal interaction length correction for precomputed accessibility
+  data was one to large (wrong dangling end computation for maximally long RRIs)
+  (thanks to Sabine Reisser)
+- BUGFIX: explicit seed encodings within last 7 nucleotides (seedBP) were 
+  ignored (thanks to Sebastian Holler)
+- BUGFIX: outNoLP option was not correctly implemented (missing recursion cases)
+  and was thus missing interactions
+- BUGFIX: osx: configure adaptation to old grep version in osx
 
 ################################################################################  
 ################################################################################
 
+220110 Martin Raden
+ * configure.ac :
+   * rewrite of grep personality call to be compatible with old grep version on osx
+
+201204 Simon Bray (thanks!) :
+ * replace travis with github action
+
+210211 Martin Raden
+ * IntaRNA/SeedConstraint :
+   * constructor: bp>2 check only if no explicit seed present
+ * IntaRNA/SeedHandlerExplicit :
+   - getSeedMaxBP() : obsolete, replaced by getSeedMinBP()
+   + getSeedMinBP() : minimal number of bps within encoded seeds; used for seed
+     constraint initialization
+   * traceBackSeed() :
+     * bugfix: check for minimal seed length sufficient on one side
+ * bin/CommandLineParsing :
+   * seedBP now set to getSeedMinBP() if explicit seeds present
+ * bin/IntaRNA :
+   * exception information now motivates to send input along with report
+ + docs/recursions : recursion depictions for sanity checks of implementations
+   + PredictorMfe2d (+outNoLP)
+   + PredictorMfe2dSeed (+outNoLP)
+ * IntaRNA/PredictorMfe2dSeed :
+ * IntaRNA/PredictorMfe2dHeuristic :
+ * IntaRNA/PredictorMfe2dHeuristicSeed :
+ * IntaRNA/PredictorMfeEns2dHeuristic :
+   * bugfix outNoLP : missing recursion cases 
+ * IntaRNA/AccessibilityFromStream : 
+   * bugfix read from stream
+   * test updated
+
+201210 Martin Raden
+ * IntaRNA/AccessibilityFromStream :
+   * bugfix: max length == 1 smaller than max-accessibility-data-length due to 
+     dangling-end treatment (thanks to Sabine Reisser)
 
 ################################################################################
 ### version 3.2.1
@@ -35,6 +84,8 @@
  * bin/CommandLineParsing :
    * changing import and usage of boost::bind and boost::placeholders namespace
      (thanks to Behra Phani Rama Krishna)
+ * R/IntaRNA_plotRegions.R :
+   * replace deprecated expand_scale() with expansion() 
 
 200615 Martin Raden
  * IntaRNA/OutputConstraint :

R/IntaRNA_plotRegions.R

@@ -123,7 +123,7 @@ coveragePlot =
 	geom_density() +
 	ylab("coverage") +
 	xlab( ifelse( is.null(title) , "position" , title ) ) +
-	scale_y_continuous(position = "right", expand=expand_scale(mult = c(0, .02))) +
+	scale_y_continuous(position = "right", expand=expansion(mult = c(0, .02))) +
 	scale_x_continuous(expand = c(0, 0), limits=c(xmin,xmax));
 
 if (!is.null(title)) {

README.md

@@ -1182,17 +1182,42 @@ molecule. IntaRNA supports such data by interfacing the Vienna RNA package
 capabilities for SHAPE reactivity data incorporation, see
 Lorenz et al. ([2015](https://doi.org/10.1093/bioinformatics/btv523), [2016](https://dx.doi.org/10.1186%2Fs13015-016-0070-z)) or the
 [RNAfold manpage](https://www.tbi.univie.ac.at/RNA/RNAfold.1.html).
+To use this feature, ViennaRNA-based accessibility computation is needed, 
+i.e. `--t|qAcc=C`, which is the default mode (no action required).
 
 The SHAPE reactivity data can be provided via file using `--qShape` or
-`--tShape` for query or target sequence, respectively.
-Independently for each, it is possible
+`--tShape` for query or target sequence, respectively. The input format is a
+space-separated 3-column format providing position, nucleotide and reactivity value as
+exmemplified below.
+
+```[bash]
+    1 G 0.134
+    2 C 0.044
+    3 C 0.057
+    4 G 0.114
+    5 U 0.094
+    6 C 0.035
+    7 G 0.909
+    8 C 0.224
+    9 C 0.529
+    10 A 1.475
+```
+
+Independently for each sequence, it is possible
 to define the methods to be used to convert the data into pseudo energies and
 pairing probabilities. The respective IntaRNA arguments are
 `--qShapeMethod`|`--tShapeMethod`
 and `--qShapeConversion`|`--tShapeConversion`, which mimics the according
 tool arguments in the Vienna RNA package (see e.g. the
 [RNAfold manpage](https://www.tbi.univie.ac.at/RNA/RNAfold.1.html)).
 
+An example call that shows the effect of SHAPE data incorporation is given below (assuming the SHAPE data from above is stored in
+the file `data-SHAPE.txt`). 
+```[bash]
+IntaRNA -q GCCGUCGCCA -t GCCGUCGCCA --tShape=data-SHAPE.txt --out=qAcc:STDOUT --out=tAcc:STDERR --out=/dev/null
+```
+
+
 For further details, please refer to our respective publication
 
 - [Integration of accessibility data from structure probing into RNA-RNA interaction prediction.](https://doi.org/10.1093/bioinformatics/bty1029)

configure.ac

@@ -1,7 +1,7 @@
 
 AC_PREREQ([2.65])
 # 5 argument version only available with aclocal >= 2.64
-AC_INIT([IntaRNA], [3.2.1], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
+AC_INIT([IntaRNA], [3.2.2], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 # minimal required version of the boost library 
 BOOST_REQUIRED_VERSION=1.50.0
@@ -411,7 +411,7 @@ AS_IF([test "$DEPENDENCYNOTFOUND" = "1"], [
 ##########################################################################
 
 # get available personalities
-AC_SUBST([PERSONALITIES],[`grep -P "^\\s+case\\s+IntaRNA\\S+\\s*:\\s*return" ./src/bin/CommandLineParsing.h | sed "s/^\\s*case\\s\\+\\(IntaRNA\\S*\\)\\s\\+:\\s\\+return.*/\\1/g" | tr "\\n" " "`])
+AC_SUBST([PERSONALITIES],[`grep "^\\s*case\\s*IntaRNA\\S*\\s*:\\s*return" ./src/bin/CommandLineParsing.h | sed "s/^\\s*case\\s\\+\\(IntaRNA\\S*\\)\\s\\+:\\s\\+return.*/\\1/g" | tr "\\n" " "`])
 ##########################################################################
 
 
@@ -476,4 +476,4 @@ You can run 'make', 'make tests' and 'make install' now!
 Run 'make install prefix=XYZ' for installation in an alternative directory.
 
 ======================================
-])
+])