v3.3.0

ChangeLog

@@ -10,6 +10,34 @@
 # changes in development version since last release 
 ################################################################################
 
+################################################################################  
+################################################################################
+
+
+################################################################################
+### version 3.3.0
+################################################################################  
+
+# IntaRNA
+- `--outPairwise` enables pairwise sequence processing instead of all-vs-all
+- input range for `--q|tIdxPos0` is now +-2,000,000,000 (was +-9,999,999) to
+  enable genomic position settings
+
+################################################################################  
+################################################################################
+
+
+220215 Martin Raden
+ * bin/CommandLineParsing :
+   + outPairwise : switch to trigger pairwise vs. all-vs-all sequence processing
+   + getQueryNumberForTarget() : target-specific query sequence number
+   + getQueryIndexForTarget() : index getter for target-specific query sequences
+ * bin/IntaRNA :
+   * query iteration now based on target-specific sequence number to enable
+     pairwise sequence processing
+220214 Martin Raden
+ * bin/CommandLineParsing :
+   * idxpos0 range now +-2,000,000,000 (was +-9,999,999) for genomic positions
 
 ################################################################################
 ### version 3.2.2

README.md

@@ -106,6 +106,7 @@ The following topics are covered by this documentation:
   - [SHAPE reactivity data to enhance accessibility computation](#shape)
 - [Output Setup](#outputSetup)
   - [Output modes](#outmodes)
+  - [Pairwise vs. all-vs-all](#outpairwise)
   - [Sequence indexing](#idxPos0)
   - [Suboptimal RNA-RNA interaction prediction and output restrictions](#subopts)
   - [Energy parameters and temperature](#energy)
@@ -1500,6 +1501,20 @@ IntaRNA --model=P --mode=M --outMode=E ...
 
 
 
+<br /><br />
+<a name="outpairwise" />
+
+## Pairwise vs. all-vs-all
+
+When multiple query and target sequences are provided, IntaRNA predicts interactions for 
+all pairs of query-target combinations, i.e. **all-vs-all**.
+
+Alternatively, you can enforce **pairwise** processing using `--outPairwise`. 
+When given, sequences are combined based on their input order, i.e. the 5th target is 
+(only) considered for interaction prediction with the 5th query sequence. Thus, you
+have to provide the same number of query and target sequences.
+
+
 <br /><br />
 <a name="idxPos0" />
 

src/bin/CommandLineParsing.cpp

@@ -106,7 +106,7 @@ CommandLineParsing::CommandLineParsing( const Personality personality  )
 
 	queryArg(""),
 	query(),
-	qIdxPos0("qIdxPos0",-9999999,9999999,1),
+	qIdxPos0("qIdxPos0",-2000000000,2000000000,1),  // 4 byte range of long = -2,147,483,648 bis 2,147,483,647
 	qSet(),
 	qSetString(""),
 	qAcc("qAcc", "NCPE", 'C'),
@@ -125,7 +125,7 @@ CommandLineParsing::CommandLineParsing( const Personality personality  )
 
 	targetArg(""),
 	target(),
-	tIdxPos0("tIdxPos0",-9999999,9999999,1),
+	tIdxPos0("tIdxPos0",-2000000000,2000000000,1),
 	tSet(),
 	tSetString(""),
 	tAcc("tAcc","NCPE", 'C'),
@@ -205,6 +205,7 @@ CommandLineParsing::CommandLineParsing( const Personality personality  )
 	outSep(";"),
 	outCsvCols(outCsvCols_default),
 	outPerRegion(false),
+	outPairwise(false),
 	outSpotProbSpots(""),
 	outNeedsZall(false),
 	outNeedsBPs(true),
@@ -992,6 +993,12 @@ CommandLineParsing::CommandLineParsing( const Personality personality  )
 						->implicit_value(true)
 	    		, "output : if given (or true), best interactions are reported independently"
 	    		" for all region combinations; otherwise only the best for each query-target combination")
+	    ("outPairwise"
+	    		, value<bool>(&outPairwise)
+						->default_value(outPairwise)
+						->implicit_value(true)
+	    		, "output : if given (or true), interactions are only computed for each corresponding query-target pair (same index) "
+	    				"instead of all-vs-all")
 	    ("verbose,v", "verbose output") // handled via easylogging++
 	    ("default-log-file", value<std::string>(&(logFileName)), "file to be used for log output (INFO, WARNING, VERBOSE, DEBUG)")
 	    ;
@@ -1190,6 +1197,11 @@ parse(int argc, char** argv)
 			parseSequences("query",qId,queryArg,query,qSet,qIdxPos0.val);
 			parseSequences("target",tId,targetArg,target,tSet,tIdxPos0.val);
 
+			// check if same number if pairwise mode
+			if (outPairwise && query.size() != target.size()) {
+				throw error("--outPairwise requires same number of query and target sequences");
+			}
+
 			// validate accessibility input from file (requires parsed sequences)
 			validate_qAccFile( qAccFile );
 			validate_tAccFile( tAccFile );
@@ -1804,6 +1816,32 @@ getQuerySequences() const
 
 ////////////////////////////////////////////////////////////////////////////
 
+const size_t
+CommandLineParsing::
+getQueryIndexForTarget( const size_t i, const size_t targetIndex ) const
+{
+	checkIfParsed();
+#if INTARNA_IN_DEBUG_MODE
+	if (i>=query.size())
+		throw std::runtime_error("CommandLineParsing::getQueryIndexForTarget("+toString(i)+") out of bounds");
+#endif
+	// depends on pairwise or all-vs-all prediction
+	return outPairwise ? targetIndex : i;
+}
+
+////////////////////////////////////////////////////////////////////////////
+
+const size_t
+CommandLineParsing::
+getQueryNumberForTarget( const size_t targetIndex ) const
+{
+	checkIfParsed();
+	// depends on pairwise or all-vs-all prediction
+	return outPairwise ? 1 : query.size();
+}
+
+////////////////////////////////////////////////////////////////////////////
+
 const CommandLineParsing::RnaSequenceVec &
 CommandLineParsing::
 getTargetSequences() const

src/bin/CommandLineParsing.h

@@ -161,6 +161,22 @@ class CommandLineParsing {
 	 */
 	const RnaSequenceVec& getQuerySequences() const;
 
+	/**
+	 * Provides the number of query sequences to be considered for a target sequence.
+	 * @param targetIndex index of the target sequence wrt. getTargetSequences().
+	 * @return the number of query sequences for this target
+	 */
+	const size_t getQueryNumberForTarget( const size_t targetIndex ) const;
+
+	/**
+	 * Provides the index (wrt. getQuerySequences()) of the i-th (wrt. getQueryNumberForTarget())
+	 * query sequence that is to be considered for a given target sequence.
+	 * @param i the i-th target-specific query sequence (wrt. getQueryNumberForTarget())
+	 * @param targetIndex index of the target sequence wrt. getTargetSequences().
+	 * @return the index of i-th query sequence (wrt. getQuerySequences()) for this target
+	 */
+	const size_t getQueryIndexForTarget( const size_t i, const size_t targetIndex ) const;
+
 	/**
 	 * Parses the target parameter and returns all parsed sequences.
 	 * @return the set of parsed target sequences
@@ -718,6 +734,9 @@ class CommandLineParsing {
 	//! for all region combinations or only the best for each query-target
 	//! combination
 	bool outPerRegion;
+	//! whether or not each query-target combinations should be considered pairwise
+	//! instead of all-vs-all
+	bool outPairwise;
 	//! for SpotProb output : spots to be tracked
 	std::string outSpotProbSpots;
 	//! whether or not Zall is needed for output generation

src/bin/IntaRNA.cpp

@@ -191,8 +191,10 @@ int main(int argc, char **argv){
 					// this parallelization should only be enabled if the outer target-loop is not parallelized
 					# pragma omp parallel for schedule(dynamic) num_threads( parameters.getThreads() ) shared(queryAcc,reportedInteractions,exceptionPtrDuringOmp,exceptionInfoDuringOmp,targetAcc,targetNumber) if(parallelizeQueryLoop)
 #endif
-					for ( size_t queryNumber = 0; queryNumber < parameters.getQuerySequences().size(); ++queryNumber )
+					for ( size_t queryIdx = 0; queryIdx < parameters.getQueryNumberForTarget(targetNumber); ++queryIdx )
 					{
+						// get index of this query wrt. getQuerySequence() and queryAcc()
+						const size_t queryNumber = parameters.getQueryIndexForTarget(queryIdx, targetNumber);
 #if INTARNA_MULITHREADING
 						#pragma omp flush (threadAborted)
 						// explicit try-catch-block due to missing OMP exception forwarding