From a9a65ed729909435f4c529a44a310392a2efd1b6 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 23 Apr 2021 13:14:53 +0200 Subject: [PATCH 01/12] energy functions expect window sub-word borders --- Extensions/typesRNAfolding.hh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Extensions/typesRNAfolding.hh b/Extensions/typesRNAfolding.hh index 3dca5630..812729cf 100644 --- a/Extensions/typesRNAfolding.hh +++ b/Extensions/typesRNAfolding.hh @@ -697,11 +697,11 @@ inline int getEnergyAtRow(const Basic_Subsequence &alignment, assert(energyFkt >= 1); assert(energyFkt <= 3); if (energyFkt == 1) { - return dli_energy(alignment.seq->row(k), alignment.i, alignment.j-1); + return dli_energy(alignment.seq->row(k), alignment.i, alignment.j-1, alignment.seq->window_right_border); } else if (energyFkt == 2) { - return dri_energy(alignment.seq->row(k), alignment.i, alignment.j-1); + return dri_energy(alignment.seq->row(k), alignment.i, alignment.j-1, alignment.seq->window_left_border); } else if (energyFkt == 3) { - return ml_mismatch_energy(alignment.seq->row(k), alignment.i, alignment.j-1); + return ml_mismatch_energy(alignment.seq->row(k), alignment.i, alignment.j-1, alignment.seq->window_right_border, alignment.seq->window_left_border); } return 0; } From 9b3e139f72a59cf6cf6031af9fdae86359b334e8 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 23 Apr 2021 13:59:05 +0200 Subject: [PATCH 02/12] check that grammar /algfunc are defined variables --- Misc/Applications/addRNAoptions.pl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Misc/Applications/addRNAoptions.pl b/Misc/Applications/addRNAoptions.pl index 4e6f0aef..97bbaa5b 100644 --- a/Misc/Applications/addRNAoptions.pl +++ b/Misc/Applications/addRNAoptions.pl @@ -24,7 +24,9 @@ sub getPath { my $content = ""; my $warn_macrostate = 0; -$warn_macrostate = 1 if ((lc($grammar) =~ m/macrostate/) and (lc($algebraproduct) =~ m/mfe|pfunc/)); +if (defined($grammar) and defined($algebraproduct)) { + $warn_macrostate = 1 if ((lc($grammar) =~ m/macrostate/) and (lc($algebraproduct) =~ m/mfe|pfunc/)); +} open (IN, $infile) || die "can't read file '$infile': $!"; my $gapcCall = ""; From dd4d934e4020f98d377b1d2254815a6b7565751e Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 26 Apr 2021 17:23:44 +0200 Subject: [PATCH 03/12] no need for borders here --- Extensions/typesRNAfolding.hh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Extensions/typesRNAfolding.hh b/Extensions/typesRNAfolding.hh index 812729cf..3dca5630 100644 --- a/Extensions/typesRNAfolding.hh +++ b/Extensions/typesRNAfolding.hh @@ -697,11 +697,11 @@ inline int getEnergyAtRow(const Basic_Subsequence &alignment, assert(energyFkt >= 1); assert(energyFkt <= 3); if (energyFkt == 1) { - return dli_energy(alignment.seq->row(k), alignment.i, alignment.j-1, alignment.seq->window_right_border); + return dli_energy(alignment.seq->row(k), alignment.i, alignment.j-1); } else if (energyFkt == 2) { - return dri_energy(alignment.seq->row(k), alignment.i, alignment.j-1, alignment.seq->window_left_border); + return dri_energy(alignment.seq->row(k), alignment.i, alignment.j-1); } else if (energyFkt == 3) { - return ml_mismatch_energy(alignment.seq->row(k), alignment.i, alignment.j-1, alignment.seq->window_right_border, alignment.seq->window_left_border); + return ml_mismatch_energy(alignment.seq->row(k), alignment.i, alignment.j-1); } return 0; } From f4d08fa44fbf394387951aa12fe58e140fa00cb5 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 12:28:17 +0200 Subject: [PATCH 04/12] adding a perl script that injects manually defined table designes for the cases of alignment-mode + window-mode + backtracing --- Misc/Applications/fix_table_design.pl | 24 ++++++++++++++++++++++++ makefile | 9 +++++++-- 2 files changed, 31 insertions(+), 2 deletions(-) create mode 100644 Misc/Applications/fix_table_design.pl diff --git a/Misc/Applications/fix_table_design.pl b/Misc/Applications/fix_table_design.pl new file mode 100644 index 00000000..d2943515 --- /dev/null +++ b/Misc/Applications/fix_table_design.pl @@ -0,0 +1,24 @@ +#!/usr/bin/env perl + +# energy functions "hl_energy", "dl_energy", "dr_energy" and "ext_mismatch_energy" of librna.so look for the previous/next base if in alignment mode up to the left/right border of the current input string. +# This is not necessarily the next character in cases where the character is a GAP. +# If in window mode, left/right borders change during sliding the window and will thus invalidate tabulated results. +# This leads to errors, if backtracing aims to recover values during the backtrace phase that have been stored in the forward phase. +# Thus, affected non-terminals *cannot* be tabulated in this combination: alignment, window-mode, backtracing. + +use strict; +use warnings; +use Data::Dumper; + +my ($gapc_file, $gapc_options) = @ARGV; + +my $tabledesign = ""; +if (($gapc_options =~ m/--window-mode/) && ($gapc_options =~ m/--k?backtrace/)) { + if ($gapc_file =~ m/ali_[nodangle|overdangle]/) { + $tabledesign = "--tab iloop --tab leftB --tab ml_comps --tab ml_comps1 --tab multiloop --tab rightB --tab stack --tab struct"; + } +} +print $tabledesign; +if ($tabledesign ne "") { + print STDERR "due to alignment mode & window mode & backtracing we will use the following table design: manualtabledesign=\"$tabledesign\"\n"; +} diff --git a/makefile b/makefile index 67f5452d..80078790 100644 --- a/makefile +++ b/makefile @@ -22,6 +22,7 @@ grammars=nodangle overdangle microstate macrostate levels=5 4 3 2 1 isEval=0 RNAOPTIONSPERLSCRIPT=/Misc/Applications/addRNAoptions.pl +FIXTABLEDESIGNSCRIPT=/Misc/Applications/fix_table_design.pl #compile options CXXFLAGS_EXTRA=-O3 -DNDEBUG @@ -89,7 +90,9 @@ test-suite: compile: if [ ! -f "$(ARCHTRIPLE)/$(PROGRAMPREFIX)$(gapc_binaryname)" ]; then \ - cd $(TMPDIR) && $(GAPC) -I $(PWD)/$(BASEDIR) -p "$(gapc_product)" $(gapc_options) $(PWD)/$(BASEDIR)/$(gapc_file); \ + cd $(TMPDIR) && \ + manualtabledesign=`$(PERL) $(PWD)/$(BASEDIR)/$(FIXTABLEDESIGNSCRIPT) $(gapc_file) "$(gapc_options)"` && \ + $(GAPC) -I $(PWD)/$(BASEDIR) -p "$(gapc_product)" $(gapc_options) $(PWD)/$(BASEDIR)/$(gapc_file) $$manualtabledesign; \ $(PERL) $(PWD)/$(BASEDIR)/$(RNAOPTIONSPERLSCRIPT) $(TMPDIR)/out.mf $(isEval) '$(gapc_binaryname)' '$(gapc_product)'; \ cd $(TMPDIR) && $(MAKE) -f out.mf CPPFLAGS_EXTRA="-I $(PWD)/$(BASEDIR) -I ./" CXXFLAGS_EXTRA="$(CXXFLAGS_EXTRA)" $(FASTLIBRNA) LDFLAGS_EXTRA="$(EXTRARUNTIMEPATHS)"; \ $(INSTALL) -d $(PWD)/$(ARCHTRIPLE); \ @@ -113,7 +116,9 @@ compile_mea: cd $(TMPDIR) && $(SED) -i "s/namespace gapc {/namespace outside_gapc {/" bppm.hh; \ cd $(TMPDIR) && $(SED) -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' bppm.hh; \ cd $(TMPDIR) && $(SED) -i 's|#include .rtlib/generic_opts.hh.|#include "Extensions/rnaoptions.hh"|' bppm.cc; \ - cd $(TMPDIR) && $(GAPC) -I $(PWD)/$(BASEDIR) -p "$(gapc_product2)" $(gapc_options2) $(PWD)/$(BASEDIR)/$(gapc_file2); \ + cd $(TMPDIR) && \ + manualtabledesign=`$(PERL) $(PWD)/$(BASEDIR)/$(FIXTABLEDESIGNSCRIPT) $(gapc_file2) "$(gapc_options2)"` && \ + $(GAPC) -I $(PWD)/$(BASEDIR) -p "$(gapc_product2)" $(gapc_options2) $(PWD)/$(BASEDIR)/$(gapc_file2) $$manualtabledesign; \ $(PERL) $(PWD)/$(BASEDIR)/$(RNAOPTIONSPERLSCRIPT) $(TMPDIR)/out.mf 2 '$(gapc_binaryname)' '$(gapc_product)'; \ cd $(TMPDIR) && $(MAKE) -f out.mf bppm.o CPPFLAGS_EXTRA="-I $(PWD)/$(BASEDIR) -I ./" CXXFLAGS_EXTRA="$(CXXFLAGS_EXTRA)" $(FASTLIBRNA) LDFLAGS_EXTRA="$(EXTRARUNTIMEPATHS)"; \ cd $(TMPDIR) && $(MAKE) -f out.mf CPPFLAGS_EXTRA="-I $(PWD)/$(BASEDIR) -I ./" CXXFLAGS_EXTRA="$(CXXFLAGS_EXTRA)" $(FASTLIBRNA) LDFLAGS_EXTRA="bppm.o $(EXTRARUNTIMEPATHS)"; \ From b9f4ace6a156ae8cb1f8cbd1bdde2889dfa1c161 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 13:15:59 +0200 Subject: [PATCH 05/12] adding table designs for other grammars --- Misc/Applications/fix_table_design.pl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/Misc/Applications/fix_table_design.pl b/Misc/Applications/fix_table_design.pl index d2943515..27706987 100644 --- a/Misc/Applications/fix_table_design.pl +++ b/Misc/Applications/fix_table_design.pl @@ -15,7 +15,13 @@ my $tabledesign = ""; if (($gapc_options =~ m/--window-mode/) && ($gapc_options =~ m/--k?backtrace/)) { if ($gapc_file =~ m/ali_[nodangle|overdangle]/) { - $tabledesign = "--tab iloop --tab leftB --tab ml_comps --tab ml_comps1 --tab multiloop --tab rightB --tab stack --tab struct"; + $tabledesign = "--tab leftB --tab ml_comps --tab ml_comps1 --tab multiloop --tab rightB --tab stack --tab strong --tab struct"; + } elsif ($gapc_file =~ m/ali_microstate/) { + $tabledesign = "--tab leftB --tab ml_comps --tab ml_comps1 --tab multiloop --tab rightB --tab stack --tab iloop --tab struct"; + } elsif ($gapc_file =~ m/ali_macrostate/) { + $tabledesign = "--tab ml_comps1 --tab no_dl_no_ss_end --tab dl_or_ss_left_ss_end --tab no_dl_ss_end --tab iloop --tab ml_comps2 --tab ml_comps4 --tab strong --tab left_dangle --tab nodangle --tab block_dl --tab dl_or_ss_left_no_ss_end --tab noleft_dangle --tab weak --tab block_dlr --tab left_unpaired --tab ml_comps3"; + } elsif ($gapc_file =~ m/ali_pKiss/) { + $tabledesign = "--tab struct --tab strong --tab weak --tab stack --tab leftB --tab rightB --tab iloop --tab multiloop --tab ml_comps --tab ml_comps1 --tab mldangle --tab pk_comps --tab middleNoDangling --tab help_pknot_free_hk --tab help_pkiss_Aleft --tab help_pkiss_Aright --tab help_pknot_free_hk_3D --tab help_pkiss_C --tab help_pkiss_D --tab knot --tab strategyA --tab strategyB --tab strategyC --tab strategyD --tab pknotsRG"; } } print $tabledesign; From 49b143aa660389be05a74165f286ba9f1ecfa949 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 13:22:02 +0200 Subject: [PATCH 06/12] can we store outs form Stefanstyle tests? --- .github/workflows/c-cpp.yml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 810e0c4f..b0f91e0f 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -5,7 +5,7 @@ on: branches: [ master ] pull_request: branches: [ master ] - + jobs: fold-grammars: strategy: @@ -17,14 +17,14 @@ jobs: - name: Install dependencies run: sudo apt-get install flex bison make libboost-all-dev libgsl-dev python3 python3-pip python3-biopython - name: clone gapc - run: git clone -b master https://github.com/jlab/gapc.git $GITHUB_WORKSPACE/../gapc + run: git clone -b fix_windowmode https://github.com/jlab/gapc.git $GITHUB_WORKSPACE/../gapc - name: configure run: cd $GITHUB_WORKSPACE/../gapc && ./configure - name: make run: cd $GITHUB_WORKSPACE/../gapc && make -j 2 - name: make install run: cd $GITHUB_WORKSPACE/../gapc && sudo make install - + - uses: actions/checkout@v2 - name: configure fold-grammars run: | @@ -39,3 +39,8 @@ jobs: cd Misc/Test-Suite/StefanStyle/ perl runTests.pl 2 ${{ matrix.task }} popd + - name: Archive test outs + uses: actions/upload-artifact@v2 + with: + name: testresults + path: Misc/Test-Suite/StefanStyle/**/*.out_noprefix From 6e89ec92263e04a261fb9e1b6da382c2ed83ed85 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 13:23:08 +0200 Subject: [PATCH 07/12] fixing syntax --- .github/workflows/c-cpp.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index b0f91e0f..29820ec5 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -43,4 +43,5 @@ jobs: uses: actions/upload-artifact@v2 with: name: testresults - path: Misc/Test-Suite/StefanStyle/**/*.out_noprefix + path: | + Misc/Test-Suite/StefanStyle/**/*.out_noprefix From 035a006e039c62465da4a3efc6ec3bcc92e7bdb4 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 13:24:29 +0200 Subject: [PATCH 08/12] fix identation --- .github/workflows/c-cpp.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 29820ec5..7b4a2a6f 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -40,8 +40,8 @@ jobs: perl runTests.pl 2 ${{ matrix.task }} popd - name: Archive test outs - uses: actions/upload-artifact@v2 - with: - name: testresults - path: | - Misc/Test-Suite/StefanStyle/**/*.out_noprefix + uses: actions/upload-artifact@v2 + with: + name: testresults + path: | + Misc/Test-Suite/StefanStyle/**/*.out_noprefix From 5c35697217c6bd3eaf6cb7846776c136da371dba Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 15:44:21 +0200 Subject: [PATCH 09/12] disentangle tests --- Misc/Test-Suite/StefanStyle/runTests.pl | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/Misc/Test-Suite/StefanStyle/runTests.pl b/Misc/Test-Suite/StefanStyle/runTests.pl index a4afc7b5..be11443f 100644 --- a/Misc/Test-Suite/StefanStyle/runTests.pl +++ b/Misc/Test-Suite/StefanStyle/runTests.pl @@ -42,14 +42,18 @@ sub getPath { checkProbing($TMPDIR, "probing.out", "probing algebra"); } if ((not defined $subTask) or ($subTask eq "shapes")) { - # runs for approx. 30min on Travis - checkProgram($TMPDIR, "rnaalishapes.run.out", "../../Applications/RNAalishapes/","RNAalishapes"); checkProgram($TMPDIR, "rnashapes.run.out", "../../Applications/RNAshapes/","RNAshapes"); } +if ((not defined $subTask) or ($subTask eq "alishapes")) { + checkProgram($TMPDIR, "rnaalishapes.run.out", "../../Applications/RNAalishapes/","RNAalishapes"); +} if ((not defined $subTask) or ($subTask eq "pkiss")) { - # runs for approx. 26min on Travis checkProgram($TMPDIR, "pkiss.run.out", "../../Applications/pKiss/","pKiss"); +} +if ((not defined $subTask) or ($subTask eq "palikiss")) { checkProgram($TMPDIR, "palikiss.run.out", "../../Applications/pAliKiss/","pAliKiss"); +} +if ((not defined $subTask) or ($subTask eq "knotinframe")) { checkProgram($TMPDIR, "knotinframe.run.out", "../../Applications/Knotinframe/","Knotinframe"); } From 4c51776382b73b8047f62c227a82ac9f1bff03ca Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 15:45:45 +0200 Subject: [PATCH 10/12] no archive + 5 instead of 3 tasks in matrix --- .github/workflows/c-cpp.yml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/.github/workflows/c-cpp.yml b/.github/workflows/c-cpp.yml index 7b4a2a6f..2a6df8b8 100644 --- a/.github/workflows/c-cpp.yml +++ b/.github/workflows/c-cpp.yml @@ -10,7 +10,7 @@ jobs: fold-grammars: strategy: matrix: - task: [default, shapes, pkiss] + task: [default, shapes, pkiss, alishapes, palikiss, knotinframe] runs-on: ubuntu-latest steps: # install gapcs @@ -39,9 +39,3 @@ jobs: cd Misc/Test-Suite/StefanStyle/ perl runTests.pl 2 ${{ matrix.task }} popd - - name: Archive test outs - uses: actions/upload-artifact@v2 - with: - name: testresults - path: | - Misc/Test-Suite/StefanStyle/**/*.out_noprefix From a6e878d92a7f956751ffd6a523912cbc1da3d224 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 16:20:27 +0200 Subject: [PATCH 11/12] window mode fixed: changes manually verified against RNAeval 2.4.17 --- .../StefanStyle/Truth/rnashapes.run.out | 305 +++++++++--------- 1 file changed, 151 insertions(+), 154 deletions(-) diff --git a/Misc/Test-Suite/StefanStyle/Truth/rnashapes.run.out b/Misc/Test-Suite/StefanStyle/Truth/rnashapes.run.out index 4e06e887..0d6e4a68 100644 --- a/Misc/Test-Suite/StefanStyle/Truth/rnashapes.run.out +++ b/Misc/Test-Suite/StefanStyle/Truth/rnashapes.run.out @@ -34,7 +34,7 @@ #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=mfe --allowLP=0 --grammar=overdangle --windowSize=40 AAGGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGUUAUGU --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --shapeLevel=5 --structureProbs=0 --temperature=37 --windowIncrement=20 >unnamed sequence 1 AAGGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGU 40 --13.70 ..(((((....))))).........(((((.....))))) [][] +-13.30 ..(((((....))))).........(((((.....))))) [][] 21 UCGUAGCAGUUGACUACUGUUAUGU 45 -9.50 .(((((((((.....))))))))). [] @@ -126,10 +126,10 @@ #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=mfe --allowLP=1 --grammar=overdangle --windowSize=40 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAA --param=BGAPDIR/share/gapc/librna/rna_turner1999.par --shapeLevel=5 --structureProbs=1 --temperature=25.9 --windowIncrement=30 >unnamed sequence 1 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGG 40 --19.58 0.4131966 ..(((((((((((...(......).....))))))))))) [] +-18.10 0.4038573 ..(((((((((((...(......).....))))))))))) [] 31 GUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAA 69 --12.24 0.1519109 ((((.((.((((......))))..))...))))...... [] +-12.07 0.1290168 ((((.((.((((......))))..))...))))...... [] #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=mfe --allowLP=1 --grammar=overdangle --windowSize=100 gGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUC --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --shapeLevel=5 --structureProbs=0 --temperature=25.9 --windowIncrement=20 >unnamed sequence @@ -364,11 +364,13 @@ #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=subopt --allowLP=1 --grammar=overdangle --windowSize=40 AAGGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGUUAUGU --absoluteDeviation=1 --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --shapeLevel=5 --structureProbs=1 --temperature=25.9 --windowIncrement=30 >unnamed sequence 1 AAGGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGU 40 --16.98 0.5022458 ..(((((....))))).........(((((.....))))) [][] --16.46 0.2093598 ..(((((....)))))..(((((.......)))))..... [][] +-16.46 0.3242941 ..(((((....)))))..(((((.......)))))..... [][] +-16.39 0.2882582 ..(((((....))))).........(((((.....))))) [][] +-15.94 0.1351810 ..(((((....))))).((((((.......))))).)... [][] 31 UGACUACUGUUAUGU 45 - -2.63 0.8337749 ((((....))))... [] + -2.46 0.7937200 ((((....))))... [] + -1.58 0.1805309 .(((....))).... [] #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=subopt --allowLP=1 --grammar=overdangle --windowSize=100 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAA --absoluteDeviation=1 --param=BGAPDIR/share/gapc/librna/rna_turner1999.par --shapeLevel=5 --structureProbs=0 --temperature=37 --windowIncrement=20 >unnamed sequence @@ -497,10 +499,10 @@ #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=shapes --allowLP=0 --grammar=overdangle --windowSize=40 gGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUC --absoluteDeviation=1 --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --shapeLevel=5 --structureProbs=1 --temperature=17 --windowIncrement=20 >unnamed sequence 1 gGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACU 40 --28.21 0.7062679 (((.((.((((....)))).)))))(((((....))))). [][] +-28.21 0.7075344 (((.((.((((....)))).)))))(((((....))))). [][] 21 CGCCUGUAGUCCCAGCUACUCGGGAGGCUC 50 --12.60 0.3642368 .(((.....((((........))))))).. [] +-12.60 0.3642399 .(((.....((((........))))))).. [] #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=shapes --allowLP=0 --grammar=overdangle --windowSize=100 gGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUC --absoluteDeviation=1 --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --shapeLevel=5 --structureProbs=1 --temperature=25.9 --windowIncrement=30 >unnamed sequence @@ -692,20 +694,15 @@ #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=probs --allowLP=0 --grammar=overdangle --windowSize=40 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAA --lowProbFilter=0.01 --outputLowProbFilter=0.0001 --param=BGAPDIR/share/gapc/librna/rna_turner1999.par --probDecimals=2 --shapeLevel=5 --structureProbs=0 --temperature=25.9 --windowIncrement=10 >unnamed sequence 1 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGG 40 --19.40 ..(((((((((((................))))))))))) 1.00 [] - - 11 GCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCU 50 - -6.87 (((.((((..........))))..)))((((.....)))) 0.76 [][] - -6.46 (((.((((..........))))..)))............. 0.24 [] +-17.92 ..(((((((((((................))))))))))) 1.00 [] 21 CCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGG 60 --10.22 ((..((.((......)).((((......))))..))..)) 0.87 [[][]] - -9.12 ........(((....((.((((......))))))..))). 0.11 [] - -8.29 ((.......))....((.((((......))))))...... 0.02 [][] + -8.95 ((..((.((......)).((((......))))..))..)) 0.56 [[][]] + -9.12 ........(((....((.((((......))))))..))). 0.44 [] 31 GUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAA 69 --12.24 ((((.((.((((......))))..))...))))...... 0.52 [] --12.05 .(((.......))).....(((((((...)))))))... 0.48 [][] +-12.05 .(((.......))).....(((((((...)))))))... 0.54 [][] +-12.07 ((((.((.((((......))))..))...))))...... 0.46 [] #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=probs --allowLP=0 --grammar=overdangle --windowSize=100 AAGGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGUUAUGU --lowProbFilter=0.01 --outputLowProbFilter=0 --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --probDecimals=2 --shapeLevel=5 --structureProbs=0 --temperature=25.9 --windowIncrement=30 >unnamed sequence @@ -806,8 +803,8 @@ #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=probs --allowLP=1 --grammar=overdangle --windowSize=40 AAGGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGUUAUGU --lowProbFilter=0.01 --outputLowProbFilter=0.0001 --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --probDecimals=2 --shapeLevel=5 --structureProbs=0 --temperature=37 --windowIncrement=10 >unnamed sequence 1 AAGGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGU 40 --13.70 ..(((((....))))).........(((((.....))))) 0.97 [][] --11.70 ..(((((....)))))((...))..(((((.....))))) 0.03 [][][] +-13.30 ..(((((....))))).........(((((.....))))) 0.98 [][] +-11.30 ..(((((....)))))((...))..(((((.....))))) 0.02 [][][] -7.60 .((((((....)))))..(((((.......)))))..).. 0.00 [[][]] 11 UCGCCCCGAGUCGUAGCAGUUGACUACUGUUAUGU 45 @@ -1045,173 +1042,173 @@ Sampling results: >unnamed sequence 1 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGG 40 100 samples, drawn by stochastic backtrace to estimate shape frequencies: --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --13.70 0.03 ..((((((((((....((..........)))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --13.70 0.03 ..((((((((((....((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.00 0.04 ..(((((((((....(((..........)))))))))))) [] --14.20 0.06 ..((((((((((..................)))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --13.70 0.03 ..((((((((((....((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --12.00 0.00 ..((((((((.....(((..........))).)))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --11.80 0.00 ..(((((((((....((............))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --14.20 0.06 ..((((((((((..................)))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --14.00 0.04 ..(((((((((....(((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --14.00 0.04 ..(((((((((....(((..........)))))))))))) [] --14.20 0.06 ..((((((((((..................)))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.00 0.04 ..(((((((((....(((..........)))))))))))) [] --14.00 0.04 ..(((((((((....(((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --12.00 0.00 ..((((((((.....(((..........))).)))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.00 0.04 ..(((((((((....(((..........)))))))))))) [] --11.60 0.00 ..((((((((((((...........))...)))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --13.70 0.03 ..((((((((((....((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] --14.70 0.14 ..((((((((....((((..........)))))))))))) [] --15.70 0.70 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-13.50 0.14 ..((((((((....((((..........)))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-10.90 0.00 ...(((((((((..................))))))))). [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-13.50 0.14 ..((((((((....((((..........)))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-12.40 0.02 ...((((((((((................)))))))))). [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-12.40 0.02 ...((((((((((................)))))))))). [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-12.50 0.03 ..((((((((((....((..........)))))))))))) [] +-13.50 0.14 ..((((((((....((((..........)))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-13.00 0.06 ..((((((((((..................)))))))))) [] +-12.80 0.04 ..(((((((((....(((..........)))))))))))) [] +-13.50 0.14 ..((((((((....((((..........)))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-10.10 0.00 ..(((((((.(((................))).))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-13.00 0.06 ..((((((((((..................)))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-13.50 0.14 ..((((((((....((((..........)))))))))))) [] +-13.50 0.14 ..((((((((....((((..........)))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-10.40 0.00 ..((((((((((((...........))...)))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-13.00 0.06 ..((((((((((..................)))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-12.40 0.02 ...((((((((((................)))))))))). [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-12.50 0.03 ..((((((((((....((..........)))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-13.50 0.14 ..((((((((....((((..........)))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-10.80 0.00 ..(((((((.....((((..........)))).))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-12.40 0.02 ...((((((((((................)))))))))). [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-14.50 0.68 ..(((((((((((................))))))))))) [] +-13.50 0.14 ..((((((((....((((..........)))))))))))) [] Sampling results: --15.70 0.70 ..(((((((((((................))))))))))) 1.00 [] +-14.50 0.68 ..(((((((((((................))))))))))) 1.00 [] 31 GUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAA 69 100 samples, drawn by stochastic backtrace to estimate shape frequencies: + -9.60 0.42 ...................(((((((...)))))))... [] + -7.40 0.01 ................((.(((((((...))))))))). [] + -9.60 0.42 ...................(((((((...)))))))... [] + -7.10 0.01 .........(((....)))(((((((...)))))))... [][] + -8.20 0.04 ....................((((((...)))))).... [] + -6.70 0.00 ..........((......))((((((...)))))).... [][] -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] + -7.10 0.01 ........(((......)))((((((...)))))).... [][] -9.60 0.42 ...................(((((((...)))))))... [] - -7.00 0.01 ........((((....))))((((((...)))))).... [][] - -7.90 0.03 ................((.(((((((...))))))).)) [] + -7.10 0.01 .(((.......)))..((.(((((((...))))))).)) [][] -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] - -8.50 0.07 ...................((((((.....))))))... [] - -7.90 0.03 ................((.(((((((...))))))).)) [] -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] - -8.20 0.04 ....................((((((...)))))).... [] - -7.50 0.01 ..((.......))......(((((((...)))))))... [][] + -5.60 0.00 ......((....)).....((((((.....))))))... [][] -9.60 0.42 ...................(((((((...)))))))... [] - -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] + -7.70 0.02 .(((.......))).....((((((.....))))))... [][] + -7.40 0.01 ................((.(((((((...))))))))). [] -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] + -6.80 0.00 ................((.((((((.....)))))).)) [] -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] - -7.80 0.02 ((((....((((......)))).......))))...... [] -9.60 0.42 ...................(((((((...)))))))... [] - -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] + -8.20 0.04 ....................((((((...)))))).... [] + -6.50 0.00 ........(((.....))).((((((...)))))).... [][] + -8.50 0.07 ...................((((((.....))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] - -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] - -7.20 0.01 .........((......))(((((((...)))))))... [][] + -8.50 0.07 ...................((((((.....))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] + -7.90 0.03 ........(((.....)))(((((((...)))))))... [][] -9.60 0.42 ...................(((((((...)))))))... [] + -7.90 0.03 ................((.(((((((...))))))).)) [] -9.60 0.42 ...................(((((((...)))))))... [] + -7.90 0.03 ................((.(((((((...))))))).)) [] -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] - -7.40 0.01 .(((.......)))......((((((...)))))).... [][] - -5.10 0.00 .....((........))..((((((.....))))))... [][] - -8.50 0.07 ...................((((((.....))))))... [] - -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] - -8.50 0.07 ...................((((((.....))))))... [] - -8.20 0.04 ....................((((((...)))))).... [] -9.60 0.42 ...................(((((((...)))))))... [] - -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] + -7.90 0.03 ................((.(((((((...))))))).)) [] + -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] + -8.50 0.07 ...................((((((.....))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] - -7.50 0.01 ..((.......))......(((((((...)))))))... [][] -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] - -7.50 0.01 ...................(((((.......)))))... [] -9.60 0.42 ...................(((((((...)))))))... [] + -6.80 0.00 ................((.((((((.....)))))).)) [] -9.60 0.42 ...................(((((((...)))))))... [] - -7.40 0.01 .(((.......)))......((((((...)))))).... [][] - -9.60 0.42 ...................(((((((...)))))))... [] - -6.70 0.00 ..........((......))((((((...)))))).... [][] - -8.50 0.07 ...................((((((.....))))))... [] - -5.70 0.00 .........(((......)))(((((...)))))..... [][] - -8.20 0.04 ....................((((((...)))))).... [] + -7.60 0.02 .......((((.....))))((((((...)))))).... [][] + -6.10 0.00 .........((......))((((((.....))))))... [][] -9.60 0.42 ...................(((((((...)))))))... [] + -7.90 0.03 ........(((.....)))(((((((...)))))))... [][] + -7.10 0.01 ........(((......)))((((((...)))))).... [][] + -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] -9.60 0.42 ...................(((((((...)))))))... [] - -7.00 0.01 ........((((......))))((((...))))...... [][] - -8.50 0.07 ...................((((((.....))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] -7.60 0.02 .......((((.....))))((((((...)))))).... [][] - -6.90 0.01 ((((.((.((((......))))..))...))))...... [] + -7.00 0.01 ((((.((.((((......))))..))...))))...... [] -9.60 0.42 ...................(((((((...)))))))... [] -9.60 0.42 ...................(((((((...)))))))... [] -7.70 0.02 .(((.......))).....((((((.....))))))... [][] @@ -1234,7 +1231,7 @@ Sampling results: -9.60 0.42 ...................(((((((...)))))))... [] -7.60 0.02 .......((((.....))))((((((...)))))).... [][] -9.60 0.42 ...................(((((((...)))))))... [] - -7.80 0.02 ((((....((((......)))).......))))...... [] + -7.90 0.03 ((((....((((......)))).......))))...... [] -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] -8.80 0.11 .(((.......))).....(((((((...)))))))... [][] -9.60 0.42 ...................(((((((...)))))))... [] @@ -1255,8 +1252,8 @@ Sampling results: Sampling results: - -9.60 0.42 ...................(((((((...)))))))... 0.71 [] - -8.80 0.11 .(((.......))).....(((((((...)))))))... 0.29 [][] + -9.60 0.42 ...................(((((((...)))))))... 0.73 [] + -8.80 0.11 .(((.......))).....(((((((...)))))))... 0.27 [][] #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=sample --allowLP=0 --grammar=overdangle --windowSize=100 AAGGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGUUAUGU --numSamples=10 --outputLowProbFilter=0.1 --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --probDecimals=2 --shapeLevel=5 --showSamples=0 --structureProbs=1 --temperature=37 --windowIncrement=10 >unnamed sequence @@ -2125,7 +2122,7 @@ Sampling results: -27.18 ((((((((((((......))))))))..).)))....... 0.3200000 [] 31 CCCAGCUACUCGGGAGGCUC 50 - -6.37 (((........)))...... 1.0000000 [] + -6.18 (((........)))...... 1.0000000 [] #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/RNAshapes --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=sample --allowLP=1 --grammar=overdangle --windowSize=100 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAA --numSamples=10 --outputLowProbFilter=0.1 --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --probDecimals=2 --shapeLevel=5 --showSamples=1 --structureProbs=1 --temperature=37 --windowIncrement=10 >unnamed sequence From afa2296a6e67b003126ebfce5bb1e16242009df8 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Tue, 27 Apr 2021 16:39:27 +0200 Subject: [PATCH 12/12] changes due to fixing window mode --- .../StefanStyle/Truth/palikiss.run.out | 23 +++++++++---------- 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/Misc/Test-Suite/StefanStyle/Truth/palikiss.run.out b/Misc/Test-Suite/StefanStyle/Truth/palikiss.run.out index 3db88de1..bfb6cf42 100644 --- a/Misc/Test-Suite/StefanStyle/Truth/palikiss.run.out +++ b/Misc/Test-Suite/StefanStyle/Truth/palikiss.run.out @@ -57,7 +57,7 @@ (-13.95 = -10.97 + -2.98) ...[[......................{{....]]..}}. (sci: 0.470) 91 G_UCGUCCCCGCGCCUGG________________G_U___ 130 -(-18.42 = -16.47 + -1.95) ..[[[..{{]]]....}}...................... (sci: 0.540) +(-18.38 = -16.43 + -1.95) ..[[[..{{]]]....}}...................... (sci: 0.540) 121 ____G_U________CUGGG_____GCCCGAGGAGACA__ 160 ( 0.00 = 0.00 + 0.00) ........................................ (sci: 0.000) @@ -79,7 +79,7 @@ (-34.91 = -30.93 + -3.98) ..[[[[.{{..]]]]............(((...[[..{{]].....}}.....................................)))...}}....... (sci: 0.380) 81 -----u-GKMkcUCGUCCCYSHRHHYRrawugmag-camryarurmY-wwyggurCUKKR-aummGMMYGRRGARACWc-MYRCrmaaa 169 -(-28.66 = -25.90 + -2.76) .......[[....{{..]]..}}[[........................................{{....]].........}}..... (sci: 0.360) +(-28.65 = -25.89 + -2.76) .......[[....{{..]]..}}[[........................................{{....]].........}}..... (sci: 0.360) #CMD: perl -I ../../Applications/lib/ x86_64-linux-gnu/pAliKiss --binPath='x86_64-linux-gnu/x86_64-linux-gnu/' --mode=subopt --allowLP=0 ROOTDIR/Misc/Test-Suite/StefanStyle/t-box.aln --Hpenalty=-12 --Kpenalty=-20 --absoluteDeviation=1 --cfactor=1.1 --consensus=consensus --minHairpinLength=6 --nfactor=1 --pairingFraction=-150 --param=BGAPDIR/share/gapc/librna/rna_turner2004.par --ribosumscoring=1 --sci=1 --shapeLevel=5 --strategy=C --temperature=25.9 --windowIncrement=10 1 ___________GCGGCCGCGCGUCGGC_G_GGGG_CAAGCGGGGUGGUACCGCGGCGCU__CGCGCACCG_GCG_____________GGCG_UCGUCCCCGCGCCUGG________________G_U________CUGGG_____GCCCGAGGAGACA__ACGCG____ 169 @@ -94,16 +94,15 @@ (-20.13 = -18.84 + -1.29) ...........[[.{{.]][[..{{]]....}}.....}} (sci: 0.570) 21 CGUCGGC_G_GGGG_CAAGCGGGGUGGUACCGCGGCGCU_ 60 -(-35.57 = -30.86 + -4.71) [[[..{{...]]].....}}..[[[.{{]]]...}}.... (sci: 0.880) +(-35.47 = -30.76 + -4.71) [[[..{{...]]].....}}..[[[.{{]]]...}}.... (sci: 0.880) 41 GGGGUGGUACCGCGGCGCU__CGCGCACCG_GCG______ 80 (-27.91 = -23.74 + -4.17) ..[[[.{{]]][[.{{]]......}}.....}}....... (sci: 0.790) -(-26.96 = -23.37 + -3.59) ..[[[.{{]]][[.{{]]....}}.......}}....... (sci: 0.760) (-26.93 = -23.82 + -3.11) .[[..{{{.]][[.{{]]....}}..}}}........... (sci: 0.760) 61 _CGCGCACCG_GCG_____________GGCG_UCGUCCCC 100 -(-12.27 = -10.06 + -2.21) ...[[......................{{....]]..}}. (sci: 0.470) -(-11.98 = -9.87 + -2.11) ...[[......................{{....]]...}} (sci: 0.460) +(-12.21 = -10.00 + -2.21) ...[[......................{{....]]..}}. (sci: 0.470) +(-11.92 = -9.81 + -2.11) ...[[......................{{....]]...}} (sci: 0.460) (-11.60 = -11.37 + -0.23) ....[[.....{{]]...................}}.... (sci: 0.440) (-11.48 = -10.82 + -0.66) ...........[[[.............{{....]]]..}} (sci: 0.440) (-11.44 = -10.92 + -0.52) ............[[.............{{]]......}}. (sci: 0.440) @@ -214,19 +213,19 @@ 41 RGGGUGGUACCGCGKBDYY--cgCGYAYYDrGMgya---- 80 ( -8.35 = -1.23 + -7.12) ..(((...)))(((.........))).............. best 'nested structure' -(-39.16 = -35.58 + -3.58) ..[[[.[[...{{.]]......}}{{]]]..}}....... best 'H-type pseudoknot' +(-39.07 = -35.49 + -3.58) ..[[[.[[...{{.]]......}}{{]]]..}}....... best 'H-type pseudoknot' no structure available best 'K-type pseudoknot' no structure available best 'H- and K-type pseudoknot' 61 -cgCGYAYYDrGMgya---------u-GKMkcUCGUCCCY 100 -( -0.07 = 0.98 + -1.05) ...(((.....))).......................... best 'nested structure' -(-19.87 = -17.17 + -2.70) ...[[......................{{....]]..}}. best 'H-type pseudoknot' +( 0.00 = 0.00 + 0.00) ........................................ best 'nested structure' +(-19.83 = -17.13 + -2.70) ...[[......................{{....]]..}}. best 'H-type pseudoknot' no structure available best 'K-type pseudoknot' no structure available best 'H- and K-type pseudoknot' 81 -----u-GKMkcUCGUCCCYSHRHHYRrawugmag-camr 120 ( -0.07 = 1.95 + -2.02) .............((....))................... best 'nested structure' -(-23.20 = -21.35 + -1.85) .............[[..{{]].....}}............ best 'H-type pseudoknot' +(-23.10 = -21.25 + -1.85) .............[[..{{]].....}}............ best 'H-type pseudoknot' no structure available best 'K-type pseudoknot' no structure available best 'H- and K-type pseudoknot' @@ -391,7 +390,7 @@ (-31.07 = -32.14 + 1.07) ...........[[....{{..[[..{{...]]...[[.....{{]]...}}...}}........]]............................}}.... (sci: 0.310) [{[{][{]}}]} 21 HNWHNKH-guRBGGuCAAGCRGGGUGGUACCGCGKBDYY--cgCGYAYYDrGMgya---------u-GKMkcUCGUCCCYSHRHHYRrawugmag-camr 120 -(-34.22 = -34.80 + 0.58) .[[.{{....]]...[[..{{{{{]]....[[.{{........]]...........................}}..}}}}}..}}............... (sci: 0.350) [{][{][{]}}} +(-34.16 = -34.74 + 0.58) .[[.{{....]]...[[..{{{{{]]....[[.{{........]]...........................}}..}}}}}..}}............... (sci: 0.350) [{][{][{]}}} 41 RGGGUGGUACCGCGKBDYY--cgCGYAYYDrGMgya---------u-GKMkcUCGUCCCYSHRHHYRrawugmag-camryarurmY-wwyggurCUKKR 140 (-18.19 = -18.48 + 0.29) .[[..{{..]].(((.....................................)))...}}........................................ (sci: 0.210) [{]()} @@ -459,7 +458,7 @@ (-78.63 = -68.74 + -9.89) .....[[.{{{{..]]...}}}}[[.......{{{{.]]..}}}}..................[[..{{]].....}}...................... (sci: 0.660) 1.0000000 [{]}[{]}[{]} 61 _CGCGCACCG_GCG_____________GGCG_UCGUCCCCGCGCCUGG________________G_U________CUGGG_____GCCCGAGGAGACA__ 160 -(-24.23 = -21.23 + -3.00) ..((((.....))))..................[[..{{]].....}}.................................................... (sci: 0.230) 0.9512897 ()[{]} +(-22.23 = -20.29 + -1.94) .................................[[..{{]].....}}.................................................... (sci: 0.210) 0.9927928 [{]} 91 G_UCGUCCCCGCGCCUGG________________G_U________CUGGG_____GCCCGAGGAGACA__ACGCG____ 169 (-22.23 = -20.29 + -1.94) ...[[..{{]].....}}............................................................. (sci: 0.270) 0.9405870 [{]}