Merge pull request #82 from BackofenLab/intarna-2

v2.0.4

ChangeLog

@@ -1,4 +1,16 @@
 
+version 2.0.4
+
+170706 Martin Mann :
+ * IntaRNA/OutputHandlerCsv :
+   + E_hybrid : hybrid-only energy = E - ED1 - ED2
+   + E_norm : length-normalized energy = E / ln( length1*length2 )
+   + E_hybridNorm : length-normalized hybrid-only energy =  E_hybrid / ln(l1*l2)
+
+170705 Martin Mann :
+ * perl/Intarna*.pl :
+   * shebang corrected
+
 170503 Martin Mann :
  * README.md :
    * output file description updated

README.md

@@ -598,6 +598,9 @@ are
 - `E_dangleR` : dangling end contribution of base pair (end1,start2)
 - `E_endL` : penalty of closing base pair (start1,end2)
 - `E_endR` : penalty of closing base pair (end1,start2)
+- `E_hybrid` : energy of hybridization only = E - ED1 - ED2
+- `E_norm` : length normalized energy = E / ln(length(seq1)*length(seq2))
+- `E_hybridNorm` : length normalized energy of hybridization only = E_hybrid / ln(length(seq1)*length(seq2))
 - `seedStart1` : start index of the seed in seq1
 - `seedEnd1` : end index of the seed in seq1
 - `seedStart2` : start index of the seed in seq2

configure.ac

@@ -2,7 +2,7 @@
 
 AC_PREREQ([2.65])
 # 5 argument version only available with aclocal >= 2.64
-AC_INIT( [IntaRNA], [2.0.3], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
+AC_INIT( [IntaRNA], [2.0.4], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 
 # minimal required version of the boost library 

perl/IntaRNA_1ui.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/env/perl -w
+#!/usr/bin/env perl
 
 use strict;
 use Getopt::Std;

perl/IntaRNA_up_1ui.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/env/perl -w
+#!/usr/bin/env perl
 
 use strict;
 use Getopt::Std;

src/IntaRNA/OutputHandlerCsv.cpp

@@ -199,6 +199,18 @@ add( const Interaction & i )
 				out <<contr.endRight;
 				break;
 
+			case E_hybrid:
+				out <<(i.energy - contr.ED1 - contr.ED2);
+				break;
+
+			case E_norm:
+				out <<(i.energy / std::log( energy.size1() * energy.size2() ) );
+				break;
+
+			case E_hybridNorm:
+				out <<( (i.energy - contr.ED1 - contr.ED2) / std::log( energy.size1() * energy.size2() ) );
+				break;
+
 			case seedStart1:
 				if (i.seed == NULL) {
 					out <<std::numeric_limits<E_type>::signaling_NaN();

src/IntaRNA/OutputHandlerCsv.h

@@ -49,6 +49,9 @@ class OutputHandlerCsv : public OutputHandler
 		E_dangleR, //!< dangling end contribution of base pair (end1,start2)
 		E_endL, //!< penalty of closing base pair (start1,end2)
 		E_endR, //!< penalty of closing base pair (end1,start2)
+		E_hybrid, //!< energy of hybridization only = E - ED1 - ED2
+		E_norm, //!< length normalized energy = E/ln(length(seq1)*length(seq2))
+		E_hybridNorm, //!< length normalized energy of hybridization only = E_hybrid / ln(length(seq1)*length(seq2))
 		seedStart1, //!< start index of the seed in seq1
 		seedEnd1, //!< end index of the seed in seq1
 		seedStart2, //!< start index of the seed in seq2
@@ -109,6 +112,9 @@ class OutputHandlerCsv : public OutputHandler
 			colType2string[E_dangleR] = "E_dangleR";
 			colType2string[E_endL] = "E_endL";
 			colType2string[E_endR] = "E_endR";
+			colType2string[E_hybrid] = "E_hybrid";
+			colType2string[E_norm] = "E_norm";
+			colType2string[E_hybridNorm] = "E_hybridNorm";
 			colType2string[seedStart1] = "seedStart1";
 			colType2string[seedEnd1] = "seedEnd1";
 			colType2string[seedStart2] = "seedStart2";

src/bin/CommandLineParsing.cpp

@@ -435,7 +435,7 @@ CommandLineParsing::CommandLineParsing()
 				->default_value(outCsvCols,"see text")
 				->notifier(boost::bind(&CommandLineParsing::validate_outCsvCols,this,_1))
 			, std::string("output : comma separated list of CSV column IDs to print if outMode=CSV."
-					" An empty argument prints all possible columns from the following available ID list: "
+					" An empty argument (using '') prints all possible columns from the following available ID list: "
 					+ boost::replace_all_copy(OutputHandlerCsv::list2string(OutputHandlerCsv::string2list("")), ",", ", ")+"."
 					+ "\nDefault = '"+outCsvCols+"'."
 					).c_str())