Mercurial > repos > rnateam > locarna_multiple
changeset 3:7554c0df9139 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 10ccc47885ce71e602d66e157bd475f1facbd042
| author | bgruening |
|---|---|
| date | Mon, 05 Dec 2022 14:28:49 +0000 |
| parents | 94b0468f0db8 |
| children | 6e20ad2c8752 |
| files | locarna.tar.bz2 locarna_multiple.xml macros.xml test-data/archaea-default.stdout test-data/archaea_relplot.scr test-data/haca.snoRNA-c.aln test-data/haca.snoRNA-default.stdout test-data/haca.snoRNA.aln test-data/tRNA_2.aln test-data/tRNA_2.epms |
| diffstat | 10 files changed, 129 insertions(+), 158 deletions(-) [+] |
line wrap: on
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--- a/locarna_multiple.xml Sat Jan 21 17:38:28 2017 -0500 +++ b/locarna_multiple.xml Mon Dec 05 14:28:49 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@VERSION@.1"> +<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description> Multiple Alignment and Folding of RNAs (mlocarna) </description> @@ -22,7 +22,8 @@ #end if --tgtdir mlocarna_results - --width 60 + ## maybe reenable later? see https://github.com/s-will/LocARNA/issues/77 + ## --width 60 ## -------------------- alignment mode and specific options # @@ -65,10 +66,9 @@ @STDOUT_ARGS@ - #if 'clustal_strict' in str($outputs).split(",") + #if 'strict' in str($outputs).split(",") && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln #end if - ]]></command> <inputs> @@ -93,8 +93,7 @@ help="Note that local alignment mode usually requires to turn off the 'max-diff' heuristic (maximal difference for alignment traces)." > - <option value="global_locarna">Global alignment - (LocARNA)</option> + <option value="global_locarna">Global alignment (LocARNA)</option> <option value="local_locarna">Local alignment (LocARNA)</option> <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option> <option value="sparse">Global fast alignment (SPARSE)</option> @@ -129,46 +128,33 @@ <expand macro="common_heuristic_parameters_sparse" /> </section> </when> - </conditional> - - <param name="outputs" type="select" display="checkboxes" multiple="True" + <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options"> - <option value="clustal_strict" selected="True">Output alignment - in ClustalW format</option> - <option value="clustal" selected="False">Output alignment - in constraint-annotated ClustalW format</option> - <option value="stockholm" selected="False">Output - alignment in Stockholm format</option> - <option value="pp" selected="False">Output - alignment in LocARNA's PP 2.0 format</option> - <option value="mlocarna_results" selected="False"> - Output LocARNA results archive (tar.gz)</option> + <option value="strict" selected="true">Alignment in ClustalW format</option> + <option value="clustal" selected="false">Alignment in constraint-annotated ClustalW format</option> + <option value="stockholm" selected="false">Alignment in Stockholm format</option> + <option value="pp" selected="false">Alignment in LocARNA's PP 2.0 format</option> + <option value="mlocarna_results" selected="false">LocARNA results archive (tar.gz)</option> </param> - <param name="stdout_verbosity" type="select" label="Standard output verbosity"> - <option value="--quiet">Don't report standard - output</option> + <option value="--quiet">Don't report standard output</option> <option value="">Non verbose</option> <option value="--verbose">Verbose</option> <option value="--moreverbose">More verbose</option> </param> - <section name="Scoring" title="Scoring parameters"> <expand macro="common_scoring_parameters" /> </section> - <section name="Folding" title="RNA folding parameters"> <expand macro="plfolding_parameters" /> <expand macro="common_folding_parameters" /> <expand macro="alifold_consensus_parameter" /> </section> - <section name="Heuristics" title="Heuristic parameters"> <expand macro="common_heuristic_parameters" /> <expand macro="max_diff_parameters_aln" /> </section> - <section name="Constraints" title="Constraint parameters"> <expand macro="bed_anchors" /> <expand macro="common_constraint_parameters" /> @@ -180,33 +166,59 @@ </outputs> <tests> - <test> + <test expect_num_outputs="3"> <param name="input_data" value="archaea.fa" /> <param name="stdout_verbosity" value="" /> <param name="max_diff_mode_selector" value="max-diff" /> <param name="max_diff" value="20" /> - <output name="stdout" file="archaea-default.stdout" /> + <param name="outputs" value="clustal,strict"/> + <output name="stdout" file="archaea-default.stdout" lines_diff="2" /> + <output name="clustal"> + <assert_contents> + <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> + <output name="clustal_strict"> + <assert_contents> + <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="2"> <param name="input_data" value="haca.snoRNA.fa" /> <param name="stdout_verbosity" value="" /> - <output name="stdout" file="haca.snoRNA-default.stdout" /> + <output name="stdout" file="haca.snoRNA-default.stdout" lines_diff="2" /> + <output name="clustal_strict"> + <assert_contents> + <has_text text="CLUSTAL W --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> </test> - <test> + <test expect_num_outputs="2"> <param name="input_data" value="archaea.fa" /> <param name="stdout_verbosity" value="" /> <param name="outputs" value="clustal" /> <param name="alignment_mode_selector" value="probabilistic" /> - <output name="clustal" file="archaea-probabilistic.aln" /> + <output name="stdout"> + <assert_contents> + <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> + <output name="clustal" file="archaea-probabilistic.aln" lines_diff="2"/> </test> - <test> + <test expect_num_outputs="2"> <param name="input_data" value="archaea.fa" /> <param name="stdout_verbosity" value="" /> <param name="outputs" value="clustal" /> <param name="max_diff_mode_selector" value="max-diff-aln" /> <param name="max_diff_aln" value="archaea-ref.aln" /> <param name="max_diff" value="2" /> - <output name="clustal" file="archaea-ref_result.aln" /> + <output name="stdout"> + <assert_contents> + <has_text text="mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA @TOOL_VERSION@"/> + </assert_contents> + </output> + <output name="clustal" file="archaea-ref_result.aln" lines_diff="2"/> </test> </tests>
--- a/macros.xml Sat Jan 21 17:38:28 2017 -0500 +++ b/macros.xml Mon Dec 05 14:28:49 2022 +0000 @@ -1,9 +1,12 @@ <macros> - <token name="@VERSION@">1.9.0</token> + <token name="@TOOL_VERSION@">1.9.2.3</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">21.09</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">locarna</requirement> + <requirement type="package" version="@TOOL_VERSION@">locarna</requirement> + <requirement type="package" version="4.2.2">r-base</requirement> </requirements> </xml> @@ -46,15 +49,15 @@ </xml> <xml name="common_scoring_parameters"> - <param name="struct_weight" argument="struct-weight" + <param argument="--struct-weight" label="Structure weight" type="integer" value="200" min="0" max="800" /> - <param name="indel_opening" argument="indel-opening" + <param argument="--indel-opening" label="Indel opening score" type="integer" value="-500" max="0" min="-1500" /> - <param argument="indel" label="Indel score" type="integer" + <param argument="--indel" label="Indel score" type="integer" value="-350" min="-1000" max="0" /> - <param argument="tau" type="integer" value="50" + <param argument="--tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/> @@ -78,17 +81,17 @@ </xml> <xml name="plfolding_parameters"> - <param name="plfold_span" argument="--plfold-span" + <param argument="--plfold-span" type="integer" value="150" min="-1" max="400" label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" /> - <param name="plfold_winsize" argument="--plfold-winsize" + <param argument="--plfold-winsize" type="integer" value="300" min="-1" max="800" label="Window size for local folding" /> </xml> <xml name="common_folding_parameters"> - <param name="rnafold_temperature" argument="rnafold-temperature" + <param argument="rnafold-temperature" type="float" value="37.0" min="10" max="50" label="Temperature for RNAfold (RNAfold's -T option)" /> </xml> @@ -147,16 +150,18 @@ </token> - <token name="@CONSTRAINT_ARGS@"> - ## -------------------- constraint parameters - $Constraints.lonely_pairs - + <token name="@CONSTRAINT_ARGS_WOLP@"> #if $Constraints.maxBPspan != -1 --maxBPspan $Constraints.maxBPspan #end if $Constraints.ignore_constraints </token> + <token name="@CONSTRAINT_ARGS@"> + ## -------------------- constraint parameters + $Constraints.lonely_pairs + @CONSTRAINT_ARGS_WOLP@ + </token> <token name="@STDOUT_ARGS@"> $stdout_verbosity @@ -171,7 +176,7 @@ label="Restrict alignable positions by maximum difference" help="(max-diff*)"> <option value="off">Off</option> - <option value="max-diff" selected="True">Maximal difference of aligned positions</option> + <option value="max-diff" selected="true">Maximal difference of aligned positions</option> <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option> <yield /> </param> @@ -180,12 +185,12 @@ <xml name="max_diff_parameters_standard_cases"> <when value="off" /> <when value="max-diff"> - <param name="max_diff" argument="max-diff" type="integer" + <param argument="--max-diff" type="integer" value="60" min="-1" max="300" label="Maximal difference of aligned positions" /> </when> <when value="max-diff-at-am"> - <param name="max_diff_at_am" argument="max-diff-at-am" type="integer" + <param argument="--max-diff-at-am" type="integer" value="60" min="-1" max="300" label="Maximal difference of aligned positions, only at arc match positions" /> @@ -206,13 +211,13 @@ </expand> <expand macro="max_diff_parameters_standard_cases" /> <when value="max-diff-aln"> - <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal" + <param argument="--max-diff-aln" type="data" format="clustal" label="Reference alignment" /> - <param name="max_diff" argument="max-diff" type="integer" + <param argument="--max-diff" type="integer" value="60" min="-1" max="300" label="Maximal difference of aligned positions" /> - <param name="max_diff_relax" argument="max-diff-relax" type="boolean" + <param argument="--max-diff-relax" type="boolean" truevalue="--max-diff-relax" falsevalue="" checked="False" label="Relax deviation constraints in multiple @@ -223,75 +228,79 @@ </xml> <xml name="common_heuristic_parameters"> - <param name="min_prob" argument="min-prob" type="float" value="0.0005" + <param argument="--min-prob" type="float" value="0.0005" min="0.0" max="0.2" label="Minimal / cutoff probability" /> - <param name="max_diff_am" argument="max-diff-am" + <param argument="--max-diff-am" type="integer" value="30" min="-1" max="300" label="Maximal difference for sizes of matched arcs (-1=off)" /> - <param name="max_bps_length_ratio" argument="max-bps-length-ratio" + <param argument="--max-bps-length-ratio" type="float" value="0.0" min="0.0" max="10.0" label="Maximal ratio 'number of considered base pairs' by 'sequence length' (default: 0.0 = no effect)" /> </xml> <xml name="common_heuristic_parameters_sparse"> - <param name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005" + <param argument="--prob-unpaired-in-loop-threshold" type="float" value="0.00005" min="0.0" max="0.2" label="Probability threshold for unpaired bases in loops" /> - <param name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001" + <param argument="--prob-basepair-in-loop-threshold" type="float" value="0.0001" min="0.0" max="0.2" label="Probability threshold for base pairs in loops" /> </xml> <xml name="in_loop_ratio_parameters"> - <param name="max_uil_length_ratio" argument="max-uil-length-ratio" + <param argument="--max-uil-length-ratio" type="float" value="0.0" min="0.0" max="10.0" label="Maximal ratio 'number considered unpaired bases in loops' by 'sequence length' (default: 0.0; no effect)" /> - <param name="max_bpil_length_ratio" argument="max-bpil-length-ratio" + <param argument="--max-bpil-length-ratio" type="float" value="0.0" min="0.0" max="10.0" label="Maximal ratio 'number of considered base pairs in loops' by 'sequence length' (default: 0.0; no effect)" /> </xml> <xml name="exparnap_in_loop_parameters"> - <param name="prob_unpaired_in_loop_threshold" - argument="prob_unpaired_in_loop_threshold" + <param argument="--prob_unpaired_in_loop_threshold" type="float" value="0.01" min="0.0" max="1.0" label="Probability threshold for unpaired bases in loops" /> - <param name="prob_basepair_in_loop_threshold" - argument="prob_basepair_in_loop_threshold" + <param argument="--prob_basepair_in_loop_threshold" type="float" value="0.01" min="0.0" max="1.0" label="Probability threshold for base pairs in loops" /> </xml> <xml name="alifold_consensus_parameter"> - <param name="alifold_consensus_dp" argument="alifold-consensus-dp" + <param argument="--alifold-consensus-dp" type="boolean" checked="False" truevalue="--alifold-consensus-dp" falsevalue="" label="Compute consensus dot plot by alifold" /> </xml> - <xml name="common_constraint_parameters"> - <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" - checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" /> - <param name="maxBPspan" argument="--maxBPspan" + <xml name="common_constraint_parameters_woLP"> + <yield/> + <param argument="--maxBPspan" type="integer" value="-1" min="-1" max="400" label="Maximum basepair span by RNAfold; -1 for arbitrary span" /> - <param name="ignore_constraints" argument="ignore-constraints" + <param argument="--ignore-constraints" type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue="" help="Ignore all anchor and structure constraints given in the fasta(-ish) input." /> </xml> + <xml name="common_constraint_parameters"> + <expand macro="common_constraint_parameters_woLP"> + <param argument="--noLP" name="lonely_pairs" type="boolean" truevalue="" falsevalue="--noLP" + checked="true" label="Allow lonely base-pairs"/> + </expand> + </xml> + <xml name="standard_outupt"> - <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}"> + <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout"> <filter>stdout_verbosity != '--quiet'</filter> </data> </xml> @@ -299,25 +308,25 @@ <xml name="mlocarna_outputs"> <expand macro="standard_outupt" /> <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln" - label="${tool.name} alignment (annotated clustal) on ${on_string}"> + label="${tool.name} on ${on_string}: alignment (annotated clustal)"> <filter>'clustal' in outputs</filter> </data> <data format="clustal" name="clustal_strict" from_work_dir="mlocarna_results/results/result.strict-aln" - label="${tool.name} alignment (clustal) on ${on_string}"> - <filter>'clustal_strict' in outputs</filter> + label="${tool.name} on ${on_string}: alignment (clustal)"> + <filter>'strict' in outputs</filter> </data> <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk" - label="${tool.name} alignment (stockholm) on ${on_string}"> + label="${tool.name} on ${on_string}: alignment (stockholm)"> <filter>'stockholm' in outputs</filter> </data> <data format="txt" name="pp" from_work_dir="mlocarna_results/results/result.pp" - label="${tool.name} alignment (PP 2.0) on ${on_string}"> + label="${tool.name} on ${on_string}: alignment (PP 2.0)"> <filter>'pp' in outputs</filter> </data> <data format="tar.gz" name="mlocarna_results_tgz" - label="${tool.name} results archive on ${on_string}"> + label="${tool.name} on ${on_string}: results archive"> <filter>'mlocarna_results' in outputs</filter> </data> </xml> @@ -330,8 +339,5 @@ <citation type="doi">10.1186/s12859-014-0404-0</citation> </citations> </xml> - - - </macros>
--- a/test-data/archaea-default.stdout Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/archaea-default.stdout Mon Dec 05 14:28:49 2022 +0000 @@ -6,13 +6,4 @@ Perform progressive alignment ... - -vhuU AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU- -fwdB AU-GUUGGAGGGGAACCC-GU------------AAGGGACCCUCCAAGAU- -selD UUACGAUGUGCCGAACCCUUU------------AAGGGAGGCACAUCGAAA -hdrA GG--CACCACUCGAAGGC--U------------AAGCCAAAGUGGUG-CU- -vhuD GU--UCUCUCGGGAACCCGUC------------AAGGGACCGAGAGA-AC- -fruA ---CCUCGAGGGGAACCC-GA------------AAGGGACCCGAGAGG--- -fdhA CG-CCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGGCG- - -alifold ((.(((((((((...(((.................))).))))))))))). (-31.59 = -20.01 + -11.58) +alifold ((.(((((((((...(((.................))).))))))))))). (-31.36 = -20.01 + -11.34)
--- a/test-data/archaea_relplot.scr Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/archaea_relplot.scr Mon Dec 05 14:28:49 2022 +0000 @@ -48,7 +48,7 @@ par(mar=c(6,2.5,1,1)) # open plot (and draw threshold) -plot(c(0),c(0),type="l", +plot(c(0),c(0),type="l", xlab="",ylab="", xlim=the_xlim,ylim=c(0,maxy), yaxp=c(0,1,2)) @@ -87,15 +87,15 @@ colors<-c(colors,colors); if (0>0) { - + for (i in 1:0) { orientation <- signals[signal_starts[i]+signal_sizes[i]*2]; sig_y <- maxy-i*anno_space; - + for (j in 0:(signal_sizes[i]-1)) { sig_x <- c(signals[signal_starts[i]+j*2],signals[signal_starts[i]+j*2+1]); - + ## draw arrows if (orientation!=0) { the_code <- 1+(orientation+1)/2; @@ -109,9 +109,9 @@ #draw inferred on-signal hit_color <- rgb(0.1,0.6,0.1,0.9) - + if (0!=1) { - + on <- c(0,4,33,44,49); off <- c(3,20,43,48,51);
--- a/test-data/haca.snoRNA-c.aln Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/haca.snoRNA-c.aln Mon Dec 05 14:28:49 2022 +0000 @@ -1,22 +1,15 @@ -CLUSTAL W --- LocARNA 1.9.0 - -ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG -ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU -ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC -ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU -#A1 ............................................................ -#A2 ............................................................ +CLUSTAL W --- LocARNA 1.9.2.3 -ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG -ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG -ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG -ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA -#A1 ....AAAAAA.................................................. -#A2 ....123456.................................................. +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG +ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG------GCCCUGUUCCUGUGUCCCAGGCUCAG +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGC-UGGCCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA +#A1 ................................................................AAAAAA.................................................. +#A2 ................................................................123456.................................................. -ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA -ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA -ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA +ACA7 AUUGGAA-----GACACUC-UGC-----GACA +ACA30 CAACUGU-----CACUCAA-UGG-----GACA +ACA5 GGAUAAA-----UUUGGUU-ACA-----GACA ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA #A1 .............................BBB #A2 .............................123
--- a/test-data/haca.snoRNA-default.stdout Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/haca.snoRNA-default.stdout Mon Dec 05 14:28:49 2022 +0000 @@ -6,28 +6,5 @@ Perform progressive alignment ... - -ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGG -ACA30 UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU -ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGC -ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUGGGUGAC--CCU -#A1 ............................................................ -#A2 ............................................................ - -ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG -ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG -ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG -ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA -#A1 ....AAAAAA.................................................. -#A2 ....123456.................................................. - -ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA -ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA -ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA -ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA -#A1 .............................BBB -#A2 .............................123 - -alifold .((((((((........((((.(((((((......))))))).))))......))..))) - ))).............((((((.....((.....((((((((((((.....))))))))) - )))......)).....)).))))......... (-61.69 = -33.85 + -27.84) +alifold .((((((((........((((.(((((((......))))))).))))......))..)))))).............(((((((...((......((((((((((((.....))))))))) + ))).........)).))).))))......... (-62.29 = -34.50 + -27.79)
--- a/test-data/haca.snoRNA.aln Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/haca.snoRNA.aln Mon Dec 05 14:28:49 2022 +0000 @@ -1,16 +1,11 @@ -CLUSTAL W --- LocARNA 1.9.0 - -ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG -ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU -ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC -ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU +CLUSTAL W --- LocARNA 1.9.2.3 -ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG -ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG -ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG -ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA +ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG +ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG +ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG------GCCCUGUUCCUGUGUCCCAGGCUCAG +ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGC-UGGCCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA -ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA -ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA -ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA +ACA7 AUUGGAA-----GACACUC-UGC-----GACA +ACA30 CAACUGU-----CACUCAA-UGG-----GACA +ACA5 GGAUAAA-----UUUGGUU-ACA-----GACA ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
--- a/test-data/tRNA_2.aln Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/tRNA_2.aln Mon Dec 05 14:28:49 2022 +0000 @@ -1,7 +1,4 @@ -CLUSTAL W --- LocARNA 1.9.0 --- Score: 2875 +CLUSTAL W --- LocARNA 1.9.2.3 --- Score: 2587 -D10744 GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGG -AF008220 GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCG - -D10744 UGAGUUCGAAUCUCACAUUUUCCG -AF008220 GCGGUUCGAGCCCGUCAUCCUCCA +D10744 GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG +AF008220 GGAGGAUUAGC--UCAGCUGGGAGAGCAUCUGCCUUA-------CAAGCAGAGGGUCGGCG-GUUCGAGCCCGUCAUCCUCCA
--- a/test-data/tRNA_2.epms Sat Jan 21 17:38:28 2017 -0500 +++ b/test-data/tRNA_2.epms Mon Dec 05 14:28:49 2022 +0000 @@ -1,4 +1,4 @@ epm_id score structure positions -0 3583 ((())) 1:4 2:5 3:6 80:67 81:68 82:69 +0 3587 ((())) 1:4 2:5 3:6 80:67 81:68 82:69 1 3593 ((())) 1:1 2:2 3:3 80:70 81:71 82:72