Merge pull request #181 from BackofenLab/dev

v3.2.0

Author: martin-raden

ChangeLog

@@ -10,9 +10,84 @@
 # changes in development version since last release 
 ################################################################################
 
+
+
 ################################################################################  
 ################################################################################
 
+################################################################################
+### version 3.2.0
+################################################################################  
+
+# IntaRNA
+- BUGFIX: accessibility blocking constraints were only applied to seed location
+- improved Zall estimate (and depending values) for `--model=X` (default)
+- new arguments:
+  - `qId|tId` : optional id (FASTA prefix) setup for sequence naming
+  - `acc|accW|accL` : meta accessibility setup for both query and target
+  - `intLenMax|intLoopMax` : meta interaction and interior loop length setup
+  
+# CopomuS
+- Compensatory mutation selector to support interaction validation experiments
+
+################################################################################
+
+200302 Martin Raden
+ * IntaRNA/IndexRange :
+   * fromString() :
+     * bugfix: + missing parsing of negative indices 
+ * IntaRNA/InteractionEnergy :
+   * areComplementary() : 
+     + check if both positions are accessible (to avoid additional checks in
+       predictor recursions)
+ * bin/IntaRNA :
+   * ambiguous nt warning now in verbose log (was info log) 
+
+200217 Martin Raden
+ * bin/CommandLineParsing :
+   * NumericParameter : 
+   * CharParameter :
+     + isSet() : checks if value and default differ
+   + qId|tId : id (prefix) for sequence naming
+   + acc|accW|accL : meta for q|t*
+   + intLenMax|intLoopMax : meta for q|t*
+   * resetParamDefault() :
+     + overwrite value (since set to default in constructor)
+   + validate_region|shape|shapeMethod|shapeConversion : generic checks for q|t
+   + validate_seedRange : generic checks for q|t
+   + validate_numberArgumentExcludeRange() : generic check excluding a range
+   + validate_id() : checks for line breaks in q|tId
+   * parseSequences() :
+   * parseSequencesFasta() :
+     + idPrefix handling
+   - obsolete functions
+     - validate_query|target
+     - validate_qAccW|L|Constr
+     - validate_q|tRegion|Shape|ShapeMethod|ShapeConversion
+     - validate_seedQ|TRange
+   * constructor() :
+     + extended default reset for new arguments
+     * q|tAcc* arguments now hidden
+     * validation calls refactored
+     + model|acc|intLenMax|intLoopMax now general arguments
+   * parse() :
+     + additional checks for meta arguments with setup of q|t variables
+     + usage of .isSet() where appropriate
+     + check that outSep is not within id prefix in outMode=C
+     + ensure intLenMax >= seedBP
+
+200207 Martin Raden + Fabio Gutmann
+ + python/CopomuS.py : Compensatory mutation selector to support interaction
+   validation experiments
+ + python/copomus/* : utility functions of CopomuS
+ * python/README.md : links to dedicated README.md of subfolders
+
+200131 Martin Raden
+ * IntaRNA/PredictorMfe2dHeuristicSeedExtension :
+   * fillHybridE_left() :
+     + extended Zall update (additional save cases considered)
+
+
 ################################################################################
 ### version 3.1.5
 ################################################################################  

README.md

@@ -193,7 +193,7 @@ not needed to be installed separately):
 
 The data provided within the github repository
 (or within the `Source code` archives provided at the  
-[IntaRNA release page](https://github.com/BackofenLab/IntaRNA/releases))
+[IntaRNA release page](https://github.com/BackofenLab/IntaRNA/releases/latest))
 is no complete distribution and
 lacks all system specifically generated files. Thus, in order to get started with
 a fresh clone of the IntaRNA source code repository you have to run the GNU autotools
@@ -214,7 +214,7 @@ Afterwards, you can continue as if you would have downloaded an
 ## IntaRNA package distribution (e.g. `intaRNA-2.0.0.tar.gz`)
 
 When downloading an IntaRNA package distribution (e.g. `intaRNA-2.0.0.tar.gz`) from the
-[IntaRNA release page](https://github.com/BackofenLab/IntaRNA/releases), you should
+[IntaRNA release page](https://github.com/BackofenLab/IntaRNA/releases/latest), you should
 first ensure, that you have all [dependencies](#deps) installed. If so, you can
 simply run the following (assuming `bash` shell).
 ```bash
@@ -277,10 +277,10 @@ and follow either [install from github](#instgithub) or
 ### ... using pre-compiled binaries
 
 For some releases, we also provide precompiled binary packages for Microsoft Windows at the
-[IntaRNA release page](https://github.com/BackofenLab/IntaRNA/releases)
+[IntaRNA release page](https://github.com/BackofenLab/IntaRNA/releases/latest)
 that enable 'out-of-the-box' usage. If you
 want to use them:
-- [download](https://github.com/BackofenLab/IntaRNA/releases) the according ZIP archive and extract
+- [download](https://github.com/BackofenLab/IntaRNA/releases/latest) the according ZIP archive and extract
 - open a [Windows command prompt](https://www.lifewire.com/how-to-open-command-prompt-2618089)
 - [run IntaRNA](#usage)
 
@@ -331,7 +331,7 @@ brew install viennarna
 brew install doxygen
 ```
 
-Download and extract the IntaRNA source code package (e.g. `intaRNA-2.0.2.tar.gz`) from the [release page](releases/).
+Download and extract the IntaRNA source code package (e.g. `intaRNA-2.0.2.tar.gz`) from the [release page](https://github.com/BackofenLab/IntaRNA/releases/latest).
 
 ```[bash]
 ./configure CC=gcc-6 CXX=g++-6
@@ -412,9 +412,12 @@ interaction energy = -10.85 kcal/mol
 
 ```
 
-or provide (multiple) sequence(s) in [FASTA-format](#https://en.wikipedia.org/wiki/FASTA_format).
-It is possible to provide either file input or to read the FASTA input from the
-STDIN stream.
+In case you need specific RNA names in your output, you can provide ID strings 
+for each RNA using e.g. `--tId="mRNA with GC"` or `--qId="sRNA-example"`.
+
+Multiple sequences can be provided in [FASTA-format](#https://en.wikipedia.org/wiki/FASTA_format).
+It is possible to use either file input or to read the FASTA input from the
+`STDIN` stream.
 
 ```bash
 # running IntaRNA with FASTA files
@@ -497,10 +500,8 @@ mode   = M
 # no seed constraint
 noSeed = true
 # full global accessibility computation
-qAccW  = 0
-qAccL  = 0
-tAccW  = 0
-tAccL  = 0
+accW  = 0
+accL  = 0
 ``` 
 
 where you use the long parameter names without the leading `--`.
@@ -750,7 +751,7 @@ by running IntaRNA when disabling both the seed constraint
 as well as the accessibility integration using
 ```bash
 # prediction results similar to TargetScan/RNAhybrid
-IntaRNA [..] --noSeed --qAcc=N --tAcc=N
+IntaRNA [..] --noSeed --acc=N
 ```
 We *add seed-constraint support to TargetScan/RNAhybrid-like computations* by removing the
 `--noSeed` flag from the above call.
@@ -767,7 +768,7 @@ Finally, RNAup only predicts interactions for subsequences of length 25.
 All this can be setup using
 ```bash
 # prediction results similar to 'RNAup -b' (incorporating accessibility of both RNAs)
-IntaRNA --mode=M --noSeed --qAccW=0 --qAccL=0 --qIntLenMax=25 --tAccW=0 --tAccL=0 --tIntLenMax=25
+IntaRNA --mode=M --noSeed --accW=0 --accL=0 --intLenMax=25
 ```
 We *add seed-constraint support to RNAup-like computations* by removing the
 `--noSeed` flag from the above call. 
@@ -1055,10 +1056,10 @@ which results in two shorter ranges. If a range is shorter than `--seedBP`, it
 is completely removed.
 
 Finally, it is possible to restrict the overall length an interaction is allowed
-to have. This can be done independently for the query and target sequence using
-`--qIntLenMax` and `--tIntLenMax`, respectively. By setting both to 0 (default),
+to have via `--intLenMax`. This can be done independently for the query and target sequence using
+`--qIntLenMax` and `--tIntLenMax`, respectively. By setting to 0 (default),
 the smaller of the full sequence length and the maximal accessibility-window
-size (`--tAccW`, `--qAccW`) is used.
+size is used (see `--accW`, `--tAccW`, or `--qAccW`).
 
 
 
@@ -1610,8 +1611,8 @@ If no value for `--energyVRNA` is provided, the default model of the underlying
 Vienna RNA package is used (see respective documentation).
 
 To increase prediction quality and to reduce the computational complexity, the
-number of unpaired bases between intermolecular base pairs is restricted
-(similar to internal loop length restrictions in single RNA folding algorithm). The
+number of unpaired bases between intermolecular base pairs is restricted via
+`--intLoopMax` (similar to internal loop length restrictions in single RNA folding algorithm). The
 upper bound can be set independently for the query and target sequence via
 `--qIntLoopMax` and `--tIntLoopMax`, respectively, and defaults to 16.
 
@@ -1856,10 +1857,11 @@ penalty for a subsequence partaking in an interaction is given by *ED=-RT log(Pu
 where *Pu* denotes the unpaired probability of the subsequence. Within the
 IntaRNA energy model, *ED* values for both interacting subsequences are considered.
 
-Accessibility incorporation can be disabled for query or target sequences using
+To globally turn off accessibility consideration, set `--acc=N`.
+Accessibility incorporation can be disabled separately for query or target sequences using
 `--qAcc=N` or `--tAcc=N`, respectively.
 
-A setup of `--qAcc=C` or `--tAcc=C` (default) enables accessibility computation
+A setup of `--acc=C` (default, as for `--qAcc=C` and `--tAcc=C`) enables accessibility computation
 using the selected [energy model](#energy) for query or target sequences, respectively.
 
 Using `--accNoLP` and `--accNoGUend`, the consideration of lonely base pairs
@@ -1885,7 +1887,8 @@ unpaired probabilities within the window (while only intramolecular base pairs
 within the window are considered).
 
 IntaRNA enables both global as well as local unpaired probability computation.
-To this end, the sliding window length has to be specified in order to enable/disable
+To this end, the sliding window length `--accW` and the maximal base pair span 
+`--accL` (<= `--accW`) have to be specified in order to enable/disable
 local folding.
 
 ##### Use case examples global/local unpaired probability computation
@@ -1899,7 +1902,7 @@ i.e. the maximal number of positions enclosed by a base pair
 independently while respecting `AccL <= AccW`.
 ```bash
 # using global accessibilities for target and query
-IntaRNA [..] --qAccW=0 --qAccL=0 --tAccW=0 --qAccL=0
+IntaRNA [..] --accW=0 --accL=0
 # using global accessibilities for query and local ones for target
 IntaRNA [..] --qAccW=0 --qAccL=0 --tAccW=150 --qAccL=100
 ```

configure.ac

@@ -1,13 +1,13 @@
 
 AC_PREREQ([2.65])
 # 5 argument version only available with aclocal >= 2.64
-AC_INIT([IntaRNA], [3.1.5], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
+AC_INIT([IntaRNA], [3.2.0], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 # minimal required version of the boost library 
 BOOST_REQUIRED_VERSION=1.50.0
 # minimal required version of the Vienna RNA library
 VRNA_REQUIRED_VERSION=2.4.14
-# minimal required version of python interpreter
+# minimal required version of python interpreter (to install intarnapvalue)
 PYTHON_REQUIRED_VERSION=3.6
 
 
@@ -436,6 +436,7 @@ AC_CONFIG_FILES([R/Makefile])
 AC_CONFIG_FILES([python/Makefile])
 AC_CONFIG_FILES([python/bin/Makefile])
 AC_CONFIG_FILES([python/intarnapvalue/Makefile])
+AC_CONFIG_FILES([python/copomus/Makefile])
 AC_CONFIG_FILES([tests/Makefile])
 AC_CONFIG_FILES([tests/data/Makefile])
 AC_CONFIG_FILES([doc/Makefile])