changeset 3:a80f279b4ad0 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277
author bgruening
date Mon, 19 Aug 2024 18:53:00 +0000
parents e66514da3a99
children
files locarna_exparnap.xml macros.xml test-data/archaea-default.stdout test-data/archaea-probabilistic.aln test-data/archaea-ref_result.aln 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.amprobs test-data/tRNA_2.bmprobs
diffstat 12 files changed, 479 insertions(+), 432 deletions(-) [+]
line wrap: on
line diff
--- a/locarna_exparnap.xml	Mon Dec 05 13:58:16 2022 +0000
+++ b/locarna_exparnap.xml	Mon Aug 19 18:53:00 2024 +0000
@@ -2,25 +2,18 @@
     <description>
         Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
     </description>
-
     <macros>
         <import>macros.xml</import>
     </macros>
-
-    <expand macro="requirements" />
-
-    <expand macro="stdio" />
-
-    <expand macro="version" />
-
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version"/>
     <command><![CDATA[
     exparna_p
-
     '$inputA'
     '$inputB'
 
-    ## -------------------- scoring parameters
-    #
+    ## -------------------- scoring parameters -------------#
     $Scoring.no_stacking
     --alpha_1 $Scoring.alpha_1
     --alpha_2 $Scoring.alpha_2
@@ -35,8 +28,7 @@
 
     @CONSTRAINT_ARGS@
     @FOLDING_ARGS@
-    ## -------------------- other parameters
-    #
+    ## -------------------- other parameters---------------- #
     #if str($Other.subopt.subopt_selector) == "on"
         --diff-to-opt-score $Other.subopt.diff_to_opt_score
         --number-of-EPMs $Other.subopt.number_of_EPMs
@@ -49,7 +41,7 @@
     $Other.no_chaining
     --out-min-prob $Other.out_min_prob
 
-    ## -------------------- output
+    ## -------------------- output ---------------- #
 
     #if 'postscript' in str($outputs).split(",")
         --output-ps
@@ -79,7 +71,7 @@
 
     @STDOUT_ARGS@
 
-    ## -------------------- post processing
+    ## -------------------- post processing --------------#
 
     #if 'anchors-pp' in str($outputs).split(",")
         && mv anchors_pp_A.pp '$anchors_ppA'
@@ -89,161 +81,95 @@
     ]]></command>
 
     <inputs>
-        <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
-               help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
-               />
-        <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
-               help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
-               />
-
-        <param name="outputs" type="select" display="checkboxes" multiple="true"
-               label="Output options">
-            <option value="postscript" selected="false">Best EPM chain
-            as colored postscript</option>
-            <option value="anchors-fasta" selected="false">Fasta with anchor
-            constraints from chaining</option>
-            <option value="anchors-pp" selected="false">LocARNA PP
-            files merging input PPs and anchor constraints from
-            chaining</option>
-            <option value="clustal" selected="false">Chain as
-            alignment in Clustal format</option>
+        <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
+        <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
+        <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
+            <option value="postscript" selected="false">Best EPM chain as colored postscript</option>
+            <option value="anchors-fasta" selected="false">Fasta with anchor constraints from chaining</option>
+            <option value="anchors-pp" selected="false">LocARNA PP files merging input PPs and anchor constraints from chaining</option>
+            <option value="clustal" selected="false">Chain as alignment in Clustal format</option>
             <option value="epm_list" selected="false">List of the found EPMs</option>
-            <option value="chained_epm_list" selected="false">List of
-            EPMs in the best chain</option>
+            <option value="chained_epm_list" selected="false">List of EPMs in the best chain</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="" selected="true">Non verbose</option>
             <option value="--verbose">Verbose</option>
         </param>
-
         <section name="Scoring" title="Scoring parameters">
-            <param argument="--alpha_1"
-                   type="integer" value="1" min="0" max="50"
-                   label="Sequence score factor"
-                   />
-            <param argument="--alpha_2"
-                   type="integer" value="5" min="0" max="50"
-                   label="Structure score factor"
-                   />
-            <param argument="--no-stacking" type="boolean"
-                   truevalue="" falsevalue="--no-stacking"
-                   label="Add stacking terms"
-                   />
-            <param argument="--alpha_3"
-                   type="integer" value="5" min="0" max="50"
-                   label="Stacking score factor"
-                   />
-            <param argument="--struct-mismatch-score"
-                   type="integer" value="-10" min="-100" max="0"
-                   label="Score for nucleotide mismatch in base pair match"
-                   />
+            <param argument="--alpha_1" type="integer" value="1" min="0" max="50" label="Sequence score factor"/>
+            <param argument="--alpha_2" type="integer" value="5" min="0" max="50" label="Structure score factor"/>
+            <param argument="--no-stacking" type="boolean" truevalue="" falsevalue="--no-stacking" label="Add stacking terms"/>
+            <param argument="--alpha_3" type="integer" value="5" min="0" max="50" label="Stacking score factor"/>
+            <param argument="--struct-mismatch-score" type="integer" value="-10" min="-100" max="0" label="Score for nucleotide mismatch in base pair match"/>
         </section>
-
         <section name="Folding" title="RNA folding parameters">
             <expand macro="common_folding_parameters" />
         </section>
-
         <section name="Heuristics" title="Heuristic parameters">
             <expand macro="common_heuristic_parameters" />
             <expand macro="max_diff_parameters" />
             <expand macro="in_loop_ratio_parameters" />
             <expand macro="exparnap_in_loop_parameters" />
         </section>
-
         <section name="Constraints" title="Constraint parameters">
             <expand macro="common_constraint_parameters" />
         </section>
-
-
         <section name="Other" title="Other parameters">
             <conditional name="subopt">
-                <param name="subopt_selector" type="select"
-                       label="Suboptimal traceback of EPMs (exact pattern matches)"
-                       help="(--subopt)">
-                    <option value="off">Enumerate only optimal
-                    EPMs</option>
+                <param name="subopt_selector" type="select" label="Suboptimal traceback of EPMs (exact pattern matches)" help="(--subopt)">
+                    <option value="off">Enumerate only optimal EPMs</option>
                     <option value="on">Perform suboptimal traceback of EPMs</option>
                 </param>
                 <when value="off" />
                 <when value="on">
-                    <param argument="--diff-to-opt-score"
-                           type="integer" value="-1" min="-20" max="0"
-                           label="Maximum score difference to optimum" />
-                    <param argument="--number-of-EPMs"
-                           type="integer" value="100" min="1" max="10000"
-                           label="Maximal number of EPMs" />
+                    <param argument="--diff-to-opt-score" type="integer" value="-1" min="-20" max="0" label="Maximum score difference to optimum" />
+                    <param argument="--number-of-EPMs" type="integer" value="100" min="1" max="10000" label="Maximal number of EPMs" />
                 </when>
             </conditional>
 
-            <param argument="--min-score"
-                   type="integer" value="30" min="0" max="1000"
-                   label="Minimum score of EPM" />
-
-            <param argument="--inexact-struct-match" type="boolean"
-                   truevalue="--inexact-struct-match" falsevalue=""
-                   label="Allow inexact structure matches"/>
-
-            <param argument="--add-filter" type="boolean"
-                   truevalue="--add-filter" falsevalue="" checked="false"
-                   label="Apply an additional filter to enumerate only
-                          EPMs that are maximally extended (only inexact)"/>
-
-            <param argument="--no-chaining" type="boolean"
-                   truevalue="" falsevalue="--no-chaining" checked="true"
-                   label="Find best overall chain by chaining"/>
-
-            <param argument="--out-min-prob"
-                   type="float" value="0.0005" min="0" max="1"
-                   label="Minimal probability in output (min-prob overrides if smaller)"/>
-
+            <param argument="--min-score" type="integer" value="30" min="0" max="1000" label="Minimum score of EPM" />
+            <param argument="--inexact-struct-match" type="boolean" truevalue="--inexact-struct-match" falsevalue="" label="Allow inexact structure matches"/>
+            <param argument="--add-filter" type="boolean" truevalue="--add-filter" falsevalue="" checked="false" label="Apply an additional filter to enumerate only EPMs that are maximally extended (only inexact)"/>
+            <param argument="--no-chaining" type="boolean" truevalue="" falsevalue="--no-chaining" checked="true" label="Find best overall chain by chaining"/>
+            <param argument="--out-min-prob" type="float" value="0.0005" min="0" max="1" label="Minimal probability in output (min-prob overrides if smaller)"/>
         </section>
     </inputs>
 
     <outputs>
         <expand macro="standard_outupt" />
-        <data format="ps" name="ps_fileA"
-              label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
+        <data format="ps" name="ps_fileA" label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
             <filter>'postscript' in outputs</filter>
         </data>
-        <data format="ps" name="ps_fileB"
-              label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
+        <data format="ps" name="ps_fileB" label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
             <filter>'postscript' in outputs</filter>
         </data>
-        <data format="txt" name="anchors_fasta"
-              label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
+        <data format="txt" name="anchors_fasta" label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
             <filter>'anchors-fasta' in outputs</filter>
         </data>
-        <data format="txt" name="anchors_ppA"
-              label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
+        <data format="txt" name="anchors_ppA" label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
             <filter>'anchors-pp' in outputs</filter>
         </data>
-        <data format="txt" name="anchors_ppB"
-              label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
+        <data format="txt" name="anchors_ppB" label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
             <filter>'anchors-pp' in outputs</filter>
         </data>
-        <data format="clustal" name="clustal"
-              label="${tool.name} on ${on_string}: chain as alignment (clustal)">
+        <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: chain as alignment (clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
-        <data format="tabular" name="epm_list"
-              label="${tool.name} on ${on_string}: list of epms">
+        <data format="tabular" name="epm_list" label="${tool.name} on ${on_string}: list of epms">
             <filter>'epm_list' in outputs</filter>
         </data>
-        <data format="tabular" name="chained_epm_list"
-              label="${tool.name} on ${on_string}: list of epms in chain">
+        <data format="tabular" name="chained_epm_list" label="${tool.name} on ${on_string}: list of epms in chain">
             <filter>'chained_epm_list' in outputs</filter>
         </data>
     </outputs>
 
     <tests>
         <test expect_num_outputs="2">
-            <param name="inputA" value="tRNA_2-1.fa" />
-            <param name="inputB" value="tRNA_2-2.fa" />
-            <param name="outputs" value="epm_list" />
-            <output name="epm_list" file="tRNA_2.epms" />
+            <param name="inputA" value="tRNA_2-1.fa"/>
+            <param name="inputB" value="tRNA_2-2.fa"/>
+            <param name="outputs" value="epm_list"/>
+            <output name="epm_list" file="tRNA_2.epms"/>
             <output name="stdout">
                 <assert_contents>
                     <has_text text="LCSEPM preprocessing..."/>
--- a/macros.xml	Mon Dec 05 13:58:16 2022 +0000
+++ b/macros.xml	Mon Aug 19 18:53:00 2024 +0000
@@ -1,7 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.9.2.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
-    <token name="@PROFILE@">21.09</token>
+    <token name="@TOOL_VERSION@">2.0.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
 
     <xml name="requirements">
         <requirements>
--- a/test-data/archaea-default.stdout	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/archaea-default.stdout	Mon Aug 19 18:53:00 2024 +0000
@@ -1,9 +1,13 @@
-mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
-Copyright Sebastian Will
-
-Compute pair probs ...
-Compute pairwise alignments ... 
-Perform progressive alignment ...
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 2.0.1
 
 
+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            ((.(((((((((...(((.................))).))))))))))). (-31.36 = -20.01 + -11.34)
+Results written to target directory /tmp/tmpstsz4a83/job_working_directory/000/2/working/mlocarna_results.
--- a/test-data/archaea-probabilistic.aln	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/archaea-probabilistic.aln	Mon Aug 19 18:53:00 2024 +0000
@@ -1,11 +1,10 @@
-CLUSTAL W --- LocARNA 1.9.0
-
+CLUSTAL W --- LocARNA 2.0.1
 
 
-selD               UUACGAUGUGCCGAACCCUU------------UAAGGGAGGCACAUCGAAA
-vhuU               AGC-UCACAACCGAACCCAU-------------UUGGGAGGUUGUGAG-CU
-fwdB               AUG-UUGGAGGGGAACCCGU-------------AAGGGACCCUCCAAG-AU
-hdrA               GGC-ACC-ACUCGAAGGCU--------------AAGCCAAAGU-GGUG-CU
-vhuD               GUU-CUC-UCGGGAACCCGU------------CAAGGGACCGA-GAGA-AC
-fdhA               CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGG-CG
-fruA               CC-UCG--AGGGGAACCCGA-------------AAGGGACCC--GAGA-GG
+vhuU               AGC-UCACAACCGAACCCA-----U---U-----UGGGAGGUUGUGA-GCU
+fwdB               AUG-UUGGAGGGGAACCCG-----U---A-----AGGGACCCUCCAA-GAU
+selD               UUACGAUGUGCCGAACCCU-----U--UA-----AGGGAGGCACAUCGAAA
+hdrA               GGC-ACC-ACUCGAAGGCU---------A-----AGCCAAAGU-GGU-GCU
+vhuD               GUU-CUC-UCGGGAACCCG-----U--CA-----AGGGACCGA-GAG-AAC
+fruA               CC-UCGA--GGGGAACCCG-----A---A-----AGGGACCC--GAGA-GG
+fdhA               CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUG-GCG
--- a/test-data/archaea-ref_result.aln	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/archaea-ref_result.aln	Mon Aug 19 18:53:00 2024 +0000
@@ -1,5 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.0
-
+CLUSTAL W --- LocARNA 2.0.1
 
 
 vhuU               AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU-
--- a/test-data/archaea_relplot.scr	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/archaea_relplot.scr	Mon Aug 19 18:53:00 2024 +0000
@@ -1,4 +1,4 @@
-pdf("/tmp/tmp5yxSuG/files/000/dataset_2.dat",width=12,height=4,version="1.4")
+pdf("/tmp/tmpewnb251n/job_working_directory/000/2/outputs/dataset_a612ea0e-aca2-4d90-987a-39141bc61f36.dat",width=12,height=4,version="1.4")
 
 rel    <- read.table("mlocarna_results/results/result.bmreliability");
 seqrel <- rel[[2]]
@@ -112,8 +112,8 @@
 
 if (0!=1) {
 
-  on  <- c(0,4,33,44,49);
-  off <- c(3,20,43,48,51);
+  on  <- c(0,33);
+  off <- c(20,51);
 
   if (length(on)>0) {
     for (i in 1:length(on)) {
@@ -123,8 +123,8 @@
 
   ### draw on/off values
   if (0) {
-    lines(c(1,1+len),c(0.0355791,0.0355791),lty=2,lwd=1)
-    lines(c(1,1+len),c(0.702675,0.702675),lty=2,lwd=1)
+    lines(c(1,1+len),c(0.0139513,0.0139513),lty=2,lwd=1)
+    lines(c(1,1+len),c(0.656017,0.656017),lty=2,lwd=1)
   }
 }
 
--- a/test-data/haca.snoRNA-c.aln	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/haca.snoRNA-c.aln	Mon Aug 19 18:53:00 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3
+CLUSTAL W --- LocARNA 2.0.1
 
 ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
 ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
--- a/test-data/haca.snoRNA-default.stdout	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/haca.snoRNA-default.stdout	Mon Aug 19 18:53:00 2024 +0000
@@ -1,10 +1,20 @@
-mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
-Copyright Sebastian Will
-
-Compute pair probs ...
-Compute pairwise alignments ... 
-Perform progressive alignment ...
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 2.0.1
 
 
-alifold            .((((((((........((((.(((((((......))))))).))))......))..)))))).............(((((((...((......((((((((((((.....)))))))))
-                   ))).........)).))).))))......... (-62.29 = -34.50 + -27.79)
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGCUGCCACAGAAACAC--UGUGAC-----UCAUG-GGCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG--CCCAUGGGUGA-CCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#A1                ................................................................AAAAAA..................................................
+#A2                ................................................................123456..................................................
+
+ACA7               AUUGGA-----AGACACU-CUGCG-----ACA
+ACA30              CAACUG-----UCACUCA-AUGGG-----ACA
+ACA5               GGAUAA-----AUUUGGU-UACAG-----ACA
+ACA59              ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1                .............................BBB
+#A2                .............................123
+
+alifold            .((((((..........((((..(((((........)))))..))))..........)))))).............((((((.............((((((((..........)))).))
+                   ))..............)).))))......... (-53.08 = -26.63 + -26.46)
+Results written to target directory /tmp/tmpstsz4a83/job_working_directory/000/4/working/mlocarna_results.
--- a/test-data/haca.snoRNA.aln	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/haca.snoRNA.aln	Mon Aug 19 18:53:00 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3
+CLUSTAL W --- LocARNA 2.0.1
 
 ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
 ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
--- a/test-data/tRNA_2.aln	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/tRNA_2.aln	Mon Aug 19 18:53:00 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3 --- Score: 2587
+CLUSTAL W --- LocARNA 2.0.1 --- Score: 2587
 
 D10744             GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
 AF008220           GGAGGAUUAGC--UCAGCUGGGAGAGCAUCUGCCUUA-------CAAGCAGAGGGUCGGCG-GUUCGAGCCCGUCAUCCUCCA
--- a/test-data/tRNA_2.amprobs	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/tRNA_2.amprobs	Mon Aug 19 18:53:00 2024 +0000
@@ -1,108 +1,185 @@
-64 69 54 59 0.079977
-63 70 53 60 0.0158884
-63 71 53 61 0.0915855
-62 72 52 62 0.203921
-61 73 51 63 0.202155
-60 74 50 64 0.175676
-59 75 49 65 0.0815626
-39 44 33 38 0.0114647
-39 46 33 37 0.0168669
-38 47 33 38 0.0303705
-37 48 32 39 0.0111801
-37 48 31 39 0.0434528
-36 42 34 38 0.0105213
-36 42 33 37 0.0442772
-36 42 33 38 0.0150469
-36 49 30 40 0.0445378
-35 40 33 37 0.0438048
-35 40 33 38 0.0131652
-35 43 33 37 0.0482007
-35 43 33 38 0.0524118
-35 43 32 39 0.0124841
-35 44 33 38 0.0456243
-35 44 32 39 0.0111628
-35 46 33 37 0.0220704
-35 50 29 41 0.016731
-34 44 33 38 0.0275446
-34 44 32 39 0.0318614
-34 44 31 39 0.0265932
-34 45 32 39 0.0344691
-33 42 31 39 0.123358
-33 47 31 39 0.0238501
-33 48 31 39 0.207448
-33 48 30 40 0.0278532
-33 49 32 39 0.0279853
-33 49 30 40 0.0365409
-32 36 33 37 0.0659838
-32 37 33 38 0.0229925
-32 40 31 39 0.01072
-32 43 30 40 0.102105
-32 45 31 39 0.0127413
-32 45 30 40 0.0472967
-32 46 30 40 0.0814206
-32 50 29 41 0.012395
-31 38 32 39 0.0108954
-31 44 29 41 0.0212986
-31 46 29 41 0.0101171
-31 50 30 40 0.105751
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--- a/test-data/tRNA_2.bmprobs	Mon Dec 05 13:58:16 2022 +0000
+++ b/test-data/tRNA_2.bmprobs	Mon Aug 19 18:53:00 2024 +0000
@@ -1,172 +1,204 @@
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