Merge pull request #191 from BackofenLab/dev

v3.2.1
BackofenLab · Nov 27, 2020 · d4a63f0 · d4a63f0
2 parents ea591b6 + 2daa731
commit d4a63f0
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Showing 23 changed files with 111 additions and 63 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -10,11 +10,64 @@
 # changes in development version since last release 
 ################################################################################
 
-
+# IntaRNA
 
 ################################################################################  
 ################################################################################
 
+
+################################################################################
+### version 3.2.1
+################################################################################  
+
+# IntaRNA
+- support for multi-seq input when `seedQ|TRange` given
+- BUGFIX: Andronescu07 energy parameter set was not loaded by name without file
+- BUGFIX: 'outMinPu' was not fully implemented
+- BUILDFIX: non-global import of boost::bind
+
+# CopomuS :
+- exit value 0 if no favorable interaction was found
+
+################################################################################  
+
+201127 Martin Raden
+ * bin/CommandLineParsing :
+   * changing import and usage of boost::bind and boost::placeholders namespace
+     (thanks to Behra Phani Rama Krishna)
+
+200615 Martin Raden
+ * IntaRNA/OutputConstraint :
+   + maxED : maximal ED penalty of each interacting subsequence
+ * bin/CommandLineParsing :
+   * getOutputConstraint() : 
+     + energy argument to setup OutputConstraint constructor call
+ * IntaRNA/Predictor :
+   * updateZall() :
+     + check for OutputConstraint.maxED
+ * IntaRNA/PredictorMfe :
+   * updateOptima() :
+     + check for OutputConstraint.maxED
+ * IntaRNA/PredictorMfe* :
+   * obsolete OutputConstraint variable removed
+
+200602 Martin Raden
+ * bin/CommandLineParsing :
+   + sequence error information now with sequence ID rather than number
+
+200602 Martin Raden
+ * bin/CommandLineParsing :
+   + explicit seedQ|TRange check for each sequence (support for multi-seq input)
+
+200429 Martin Raden
+ * python/copomus/candidate_selectors.py :
+   * bugfix: sys.exit(0) if not favorable interaction was found
+
+200312 Martin Raden
+ * bin/CommandLineParsing :
+   * validate_energyFile() : 
+     + bugfix: missing check for predefined Andronescu07 data set name
+
 ################################################################################
 ### version 3.2.0
 ################################################################################  

diff --git a/configure.ac b/configure.ac
@@ -1,7 +1,7 @@
 
 AC_PREREQ([2.65])
 # 5 argument version only available with aclocal >= 2.64
-AC_INIT([IntaRNA], [3.2.0], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
+AC_INIT([IntaRNA], [3.2.1], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 # minimal required version of the boost library 
 BOOST_REQUIRED_VERSION=1.50.0

diff --git a/python/copomus/candidate_selectors.py b/python/copomus/candidate_selectors.py
@@ -24,7 +24,7 @@ def get_mfe_bps(query: str, target: str, qidxpos0: int, tidxpos0: int, param_fil
     data = i.run(query, target, qidxpos0, tidxpos0, 'bpList', threads, param_file=param_file)
     if not data or not data['bpList']:
         print('No favorable interaction between the specified sequences!')
-        sys.exit(1)
+        sys.exit(0)
     for t in data['bpList'].strip().split(':'):
         t_index, q_index = [int(x) for x in t.strip('(').strip(')').split(',')]
         candidates.append((q_index, t_index))  # note we do query first, then target
@@ -48,7 +48,7 @@ def get_mfe_bps_so(query: str, target: str, qidxpos0: int, tidxpos0: int, param_
     data = i.run(query, target, qidxpos0, tidxpos0, 'start1,end1,start2,end2', threads, param_file=param_file)
     if not data:
         print('No favorable interaction between the specified sequences!')
-        sys.exit(1)
+        sys.exit(0)
     data = i.run(query, target, qidxpos0, tidxpos0, 'bpList', threads, 1000, param_file,
                  ['--qRegion', f"{data['start2']}-{data['end2']}", '--tRegion',  f"{data['start1']}-{data['end1']}"])
     for subopt in data:

diff --git a/src/IntaRNA/OutputConstraint.cpp b/src/IntaRNA/OutputConstraint.cpp
@@ -15,6 +15,7 @@ OutputConstraint::OutputConstraint(
 		, const bool noGUend
 		, const bool needZall
 		, const bool needBPs
+		, const E_type maxED
 		)
  :
 	  reportMax(reportMax)
@@ -26,6 +27,7 @@ OutputConstraint::OutputConstraint(
 	, noGUend(noGUend)
 	, needZall(needZall)
 	, needBPs(needBPs)
+	, maxED(maxED)
 {
 	if(deltaE < (E_type)0.0) throw std::runtime_error("OutputConstraint(deltaE="+toString(deltaE)+") not >= 0.0");
 }

diff --git a/src/IntaRNA/OutputConstraint.h b/src/IntaRNA/OutputConstraint.h
@@ -3,6 +3,7 @@
 #define INTARNA_OUTPUTCONSTRAINT_H_
 
 #include "IntaRNA/general.h"
+#include "IntaRNA/Accessibility.h"
 
 namespace IntaRNA {
 
@@ -58,6 +59,9 @@ class OutputConstraint
 	//! whether or not interaction base pairs have to be traced for output generation
 	const bool needBPs;
 
+	//! maximal ED penalty of each interacting subsequence to be considered for output
+	const E_type maxED;
+
 public:
 
 	/**
@@ -83,7 +87,8 @@ class OutputConstraint
 						, const bool noLP = false
 						, const bool noGUend = false
 						, const bool needZall = false
-						, const bool needBPs = true );
+						, const bool needBPs = true
+						, const E_type maxED = Accessibility::ED_UPPER_BOUND);
 
 	//! destruction
 	virtual ~OutputConstraint();

diff --git a/src/IntaRNA/Predictor.h b/src/IntaRNA/Predictor.h
@@ -256,6 +256,15 @@ updateZall( const size_t i1, const size_t j1
 		return;
 	}
 
+	// check ED penalties
+	if (output.getOutputConstraint().maxED < Accessibility::ED_UPPER_BOUND
+			&& (energy.getED1(i1,j1) > output.getOutputConstraint().maxED
+					|| energy.getED2(i2,j2) > output.getOutputConstraint().maxED)
+			)
+	{
+		return;
+	}
+
 	// increment Zall with BW of overall energy
 	incrementZall(
 			energy.getBoltzmannWeight(

diff --git a/src/IntaRNA/PredictorMfe.cpp b/src/IntaRNA/PredictorMfe.cpp
@@ -92,6 +92,15 @@ updateOptima( const size_t i1, const size_t j1
 		return;
 	}
 
+	// check ED penalties
+	if (output.getOutputConstraint().maxED < Accessibility::ED_UPPER_BOUND
+			&& (energy.getED1(i1,j1) > output.getOutputConstraint().maxED
+					|| energy.getED2(i2,j2) > output.getOutputConstraint().maxED)
+			)
+	{
+		return;
+	}
+
 	// update Zall if needed
 	if (incrementZall) {
 		updateZall( i1,j1, i2,j2, interE, isHybridE );

diff --git a/src/IntaRNA/PredictorMfe2d.cpp b/src/IntaRNA/PredictorMfe2d.cpp
@@ -34,9 +34,6 @@ PredictorMfe2d::
 predict( const IndexRange & r1
 		, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
-
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfe2dHeuristic.cpp b/src/IntaRNA/PredictorMfe2dHeuristic.cpp
@@ -35,8 +35,6 @@ predict( const IndexRange & r1
 		, const IndexRange & r2
 		)
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfe2dHeuristicSeed.cpp b/src/IntaRNA/PredictorMfe2dHeuristicSeed.cpp
@@ -35,8 +35,6 @@ PredictorMfe2dHeuristicSeed::
 predict( const IndexRange & r1
 		, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfe2dHeuristicSeedExtension.cpp b/src/IntaRNA/PredictorMfe2dHeuristicSeedExtension.cpp
@@ -33,8 +33,6 @@ void
 PredictorMfe2dHeuristicSeedExtension::
 predict( const IndexRange & r1, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfe2dSeed.cpp b/src/IntaRNA/PredictorMfe2dSeed.cpp
@@ -32,8 +32,6 @@ void
 PredictorMfe2dSeed::
 predict( const IndexRange & r1, const IndexRange & r2  )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfe2dSeedExtension.cpp b/src/IntaRNA/PredictorMfe2dSeedExtension.cpp
@@ -33,8 +33,6 @@ void
 PredictorMfe2dSeedExtension::
 predict( const IndexRange & r1, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfeEns.cpp b/src/IntaRNA/PredictorMfeEns.cpp
@@ -111,8 +111,6 @@ void
 PredictorMfeEns::
 traceBack( Interaction & interaction )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 	// check if something to trace
 	if (interaction.basePairs.size() < 2) {
 		return;

diff --git a/src/IntaRNA/PredictorMfeEns2d.cpp b/src/IntaRNA/PredictorMfeEns2d.cpp
@@ -34,8 +34,6 @@ PredictorMfeEns2d::
 predict( const IndexRange & r1
 		, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfeEns2dHeuristic.cpp b/src/IntaRNA/PredictorMfeEns2dHeuristic.cpp
@@ -34,8 +34,6 @@ predict( const IndexRange & r1
 		, const IndexRange & r2
 		)
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfeEns2dHeuristicSeedExtension.cpp b/src/IntaRNA/PredictorMfeEns2dHeuristicSeedExtension.cpp
@@ -32,8 +32,6 @@ void
 PredictorMfeEns2dHeuristicSeedExtension::
 predict( const IndexRange & r1, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfeEns2dSeedExtension.cpp b/src/IntaRNA/PredictorMfeEns2dSeedExtension.cpp
@@ -33,8 +33,6 @@ void
 PredictorMfeEns2dSeedExtension::
 predict( const IndexRange & r1, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif

diff --git a/src/IntaRNA/PredictorMfeEnsSeedOnly.cpp b/src/IntaRNA/PredictorMfeEnsSeedOnly.cpp
@@ -32,8 +32,6 @@ void
 PredictorMfeEnsSeedOnly::
 predict( const IndexRange & r1, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif
@@ -97,8 +95,6 @@ void
 PredictorMfeEnsSeedOnly::
 traceBack( Interaction & interaction )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 	// check if something to trace
 	if (interaction.basePairs.size() < 2) {
 		return;

diff --git a/src/IntaRNA/PredictorMfeSeedOnly.cpp b/src/IntaRNA/PredictorMfeSeedOnly.cpp
@@ -32,8 +32,6 @@ void
 PredictorMfeSeedOnly::
 predict( const IndexRange & r1, const IndexRange & r2 )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 #if INTARNA_MULITHREADING
 	#pragma omp critical(intarna_omp_logOutput)
 #endif
@@ -95,8 +93,6 @@ void
 PredictorMfeSeedOnly::
 traceBack( Interaction & interaction )
 {
-	// temporary access
-	const OutputConstraint & outConstraint = output.getOutputConstraint();
 	// check if something to trace
 	if (interaction.basePairs.size() < 2) {
 		return;