changeset 1:a5a2d3cefce1 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author rnateam
date Fri, 13 Jan 2017 16:48:50 -0500
parents 8414fea2a6fd
children 94b0468f0db8
files locarna_multiple.xml macros.xml test-data/archaea-ref.aln test-data/archaea-ref_result.aln test-data/ferritin_human.fa test-data/ferritin_mouse.fa test-data/haca.snoRNA-1.aln test-data/haca.snoRNA-2.aln test-data/haca.snoRNA-c.aln test-data/haca.snoRNA.aln test-data/tRNA_2.amprobs test-data/tRNA_2.bmprobs test-data/tRNA_2.epms
diffstat 13 files changed, 552 insertions(+), 82 deletions(-) [+]
line wrap: on
line diff
--- a/locarna_multiple.xml	Wed Dec 28 18:52:14 2016 -0500
+++ b/locarna_multiple.xml	Fri Jan 13 16:48:50 2017 -0500
@@ -1,6 +1,6 @@
-<tool id="locarna_multiple" name="LocARNA Multiple Aligner (mlocarna)" version="@VERSION@.0">
+<tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@VERSION@.1">
     <description>
-        Multiple Alignment and Folding of RNAs
+        Multiple Alignment and Folding of RNAs (mlocarna)
     </description>
 
     <macros>
@@ -25,12 +25,12 @@
     --width 60
     
     ## -------------------- alignment mode and specific options
-
+    #
     #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
         $alignment_mode.free_endgaps
-    #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
+    #elif str($alignment_mode.alignment_mode_selector) == "local_locarna"
         --sequ-local on
-    #else if str($alignment_mode.alignment_mode_selector) == "probabilistic"
+    #elif str($alignment_mode.alignment_mode_selector) == "probabilistic"
         --probabilistic
         $alignment_mode.consistency_transformation
         
@@ -38,67 +38,27 @@
             --iterate
             --iterations $alignment_mode.iterations
         #end if
-    #else if str($alignment_mode.alignment_mode_selector) == "sparse"
+    #elif str($alignment_mode.alignment_mode_selector) == "sparse"
         --sparse
     #end if
     
-    ## -------------------- scoring parameters
-    
-    --indel $Scoring.indel
-    --indel-opening $Scoring.indel_opening
-    --struct-weight $Scoring.struct_weight
-    --tau $Scoring.tau
-    
-    #if str($Scoring.sequence_score.sequence_score_selector) == "match"
-        --match $Scoring.sequence_score.match
-        --mismatch $Scoring.sequence_score.mismatch
-    #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
-        --use-ribosum true
-    #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
-        --ribofit true
-    #end if
+    @SCORING_ARGS@
 
-    ## -------------------- folding parameters
-
+    @FOLDING_ARGS@
     #if $Folding.plfold_span>=0
         --plfold-span $Folding.plfold_span
         --plfold-winsize $Folding.plfold_winsize
     #end if
-    
-    #if float($Folding.rnafold_temperature) != 37.0
-        --rnafold-temperature $Folding.rnafold_temperature
-    #end if
-
     $Folding.alifold_consensus_dp
 
-    ## -------------------- heuristic parameters
+    @HEURISTIC_ARGS@
     
-    -p $Heuristics.min_prob
-    --max-diff-am $Heuristics.max_diff_am
-    --max-diff $Heuristics.max_diff
-    --max-diff-at-am $Heuristics.max_diff_at_am
-    --max-bps-length-ratio $Heuristics.max_bps_length_ratio
-    
-
-    ## -------------------- other parameters
-
-    #if str($Constraint.bed_anchors.bed_anchors_selector) == "yes"
-        --anchor-constraints $Constraint.bed_anchors.bed_anchors_file
+    @CONSTRAINT_ARGS@
+    #if str($Constraints.bed_anchors.bed_anchors_selector) == "yes"
+        --anchor-constraints $Constraints.bed_anchors.bed_anchors_file
     #end if
 
-    $Constraint.lonely_pairs
-
-    #if $Constraint.maxBPspan != -1
-        --maxBPspan $Constraint.maxBPspan
-    #end if
-
-    $Constraint.ignore_constraints
-
-    $stdout_verbosity
-
-    #if str($stdout_verbosity) != "--quiet":
-        > '$stdout'
-    #end if
+    @STDOUT_ARGS@
 
     #if 'clustal_strict' in str($outputs).split(",")
         && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
@@ -196,22 +156,25 @@
 
         <section name="Heuristics" title="Heuristic parameters">
             <expand macro="common_heuristic_parameters" />
+            <expand macro="max_diff_parameters_aln" />
         </section>
 
-        <section name="Constraint" title="Constraint parameters">
+        <section name="Constraints" title="Constraint parameters">
             <expand macro="bed_anchors" />
-            <expand macro="constraints" />
+            <expand macro="common_constraint_parameters" />
         </section>
     </inputs>
     
     <outputs>
-        <expand macro="common_outputs" />
+        <expand macro="mlocarna_outputs" />
     </outputs>
     
     <tests>
         <test>
             <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" />
         </test>
         <test>
@@ -226,6 +189,15 @@
             <param name="alignment_mode_selector" value="probabilistic" />
             <output name="clustal" file="archaea-probabilistic.aln" />
         </test>
+        <test>
+            <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" />
+        </test>
     </tests>
 
     <help><![CDATA[ **MLocARNA -- Multiple alignment of RNAs**
--- a/macros.xml	Wed Dec 28 18:52:14 2016 -0500
+++ b/macros.xml	Fri Jan 13 16:48:50 2017 -0500
@@ -25,14 +25,16 @@
         <conditional name="bed_anchors">
             <param name="bed_anchors_selector" type="select" label="Anchor constraints"
                    help="Anchor constraints in bed format specify positions of
-                             named anchor regions per sequence. The sequence names
-                             ('contig' names have to correspond to the fasta input
-                             sequence names. Anchor names must be unique per sequence
-                             and regions of the same name for different sequences
-                             must have the same length. This constrains the alignment
-                             to align all regions of the same name.">
-                <option value="no">Don't load anchor constraints from bed file</option> 
-                <option value="yes">Load anchor constraints from bed file</option> 
+                         named anchor regions per sequence. The sequence names
+                         ('contig' names have to correspond to the fasta input
+                         sequence names. Anchor names must be unique per sequence
+                         and regions of the same name for different sequences
+                         must have the same length. This constrains the alignment
+                         to align all regions of the same name.">
+                <option value="no">Don't load anchor constraints from
+                bed file</option>
+                <option value="yes">Load anchor constraints from bed
+                file</option>
             </param>
             <when value="no" />
             <when value="yes">
@@ -91,37 +93,176 @@
                label="Temperature for RNAfold (RNAfold's -T option)" />
     </xml>
 
+    <token name="@SCORING_ARGS@">
+        ## -------------------- scoring parameters
+        --indel $Scoring.indel
+        --indel-opening $Scoring.indel_opening
+        --struct-weight $Scoring.struct_weight
+        --tau $Scoring.tau
+        
+        #if str($Scoring.sequence_score.sequence_score_selector) == "match"
+            --match $Scoring.sequence_score.match
+            --mismatch $Scoring.sequence_score.mismatch
+        #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
+            --use-ribosum true
+        #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
+            --ribofit true
+        #end if
+    </token>
+
+    <token name="@FOLDING_ARGS@">
+        ## -------------------- folding parameters
+        #if float($Folding.rnafold_temperature) != 37.0
+            --rnafold-temperature $Folding.rnafold_temperature
+        #end if
+    </token>
+
+    <token name="@HEURISTIC_ARGS@">
+        ## -------------------- heuristic parameters
+        -p $Heuristics.min_prob
+
+        #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off"
+            --max-diff -1
+        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff"
+            --max-diff $Heuristics.max_diff_mode.max_diff
+        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am"
+            --max-diff -1
+            --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am
+        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln"
+            --max-diff $Heuristics.max_diff_mode.max_diff
+            --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln'
+            $Heuristics.max_diff_mode.max_diff_relax
+        #end if
+        
+        --max-diff-am $Heuristics.max_diff_am
+    
+        #if float($Heuristics.max_bps_length_ratio) > 0.0
+            --max-bps-length-ratio $Heuristics.max_bps_length_ratio
+        #end if
+    </token>
+
+    <token name="@CONSTRAINT_ARGS@">
+        ## -------------------- constraint parameters
+        $Constraints.lonely_pairs
+
+        #if $Constraints.maxBPspan != -1
+            --maxBPspan $Constraints.maxBPspan
+        #end if
+
+        $Constraints.ignore_constraints
+    </token>
+
+    <token name="@STDOUT_ARGS@">
+        $stdout_verbosity
+        
+        #if str($stdout_verbosity) != "--quiet":
+            > '$stdout'
+        #end if
+    </token>
+
+    <xml name="max_diff_parameters_selector">
+        <param name="max_diff_mode_selector" type="select"
+               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-at-am">Maximal difference of aligned positions at arc matches</option> 
+            <yield />
+        </param>
+    </xml>
+    
+    <xml name="max_diff_parameters_standard_cases">
+        <when value="off" />
+        <when value="max-diff">
+            <param  name="max_diff" 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" 
+                    value="60" min="-1" max="300"
+                    label="Maximal difference of aligned positions,
+                           only at arc match positions" />
+        </when>
+    </xml>
+
+    <xml name="max_diff_parameters">
+        <conditional name="max_diff_mode">
+            <expand macro="max_diff_parameters_selector" />
+            <expand macro="max_diff_parameters_standard_cases" />
+        </conditional>
+    </xml>
+
+    <xml name="max_diff_parameters_aln">
+        <conditional name="max_diff_mode">
+            <expand macro="max_diff_parameters_selector">
+                <option value="max-diff-aln">Maximal difference to a reference alignment</option>
+            </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"
+                       label="Reference alignment"
+                       />
+                <param  name="max_diff" 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"
+                       truevalue="--max-diff-relax" falsevalue=""
+                       checked="False"
+                       label="Relax deviation constraints in multiple
+                              aligmnent."
+                       />
+            </when>
+        </conditional>
+    </xml>
+
     <xml name="common_heuristic_parameters">
         <param  name="min_prob" 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" 
                 type="integer" value="30" 
                 min="-1" max="300"
-                label="Maximal difference for sizes of matched arcs (-1=off)" /> 
-
-        <param  name="max_diff" argument="max-diff" type="integer"
-                value="60" min="-1" max="300"
-                label="Maximal difference for alignment traces (-1=off)" /> 
-
-        <param  name="max_diff_at_am" argument="max-diff-am" type="integer" 
-                value="-1" min="-1" max="300"
-                label="Maximal difference for alignment traces, only at arc match positions" /> 
+                label="Maximal difference for sizes of matched arcs (-1=off)" />
         
         <param  name="max_bps_length_ratio" argument="max-bps-length-ratio"
-                type="float" value="0.0" min="0.0" max="1.0" 
-                label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" /> 
+                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="in_loop_ratio_parameters">
+        <param  name="max_uil_length_ratio" 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"
+                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"
+                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"
+                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" 
-                type="boolean" checked="false" 
+                type="boolean" checked="False" 
                 truevalue="--alifold-consensus-dp" falsevalue=""
                 label="Compute consensus dot plot by alifold" />
     </xml>
     
-    <xml name="constraints">
+    <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" 
@@ -133,13 +274,14 @@
                      in the fasta(-ish) input." />
     </xml>
 
-    <xml name="common_other_parameters">
-    </xml>
-
-    <xml name="common_outputs">
+    <xml name="standard_outupt">
         <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
             <filter>stdout_verbosity != '--quiet'</filter>
         </data>
+    </xml>
+
+    <xml name="mlocarna_outputs">
+        <expand macro="standard_outupt" />
         <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
               label="${tool.name} alignment (annotated clustal) on ${on_string}">
             <filter>'clustal' in outputs</filter>
@@ -169,6 +311,8 @@
             <citation
             type="doi">10.1371/journal.pcbi.0030065</citation>
             <citation type="doi">10.1261/rna.029041.111</citation>
+            <citation type="doi">10.1093/bioinformatics/btv185</citation>
+            <citation type="doi">10.1186/s12859-014-0404-0</citation>
         </citations>
     </xml>
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-ref.aln	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,9 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-ref_result.aln	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,11 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+
+
+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-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ferritin_human.fa	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,2 @@
+> human ferritin
+CCAGACGUUCUUCGCCGAGAGUCGUCGGGGUUUCCUGCUUCAACAGUGCUUGGACGGAACCCGGCGCUCGUUCCCCACCCCGGCCGGCCGCCCAUAGCCAGCCCUCCGUCACCUCUUCACCGCACCCUCGGACUGCCCCAAGGCCCCCGCCGCCGCUCCAGCGCCGCGCAGCCACCGCCGCCGCCGCCGCCUCUCCUUAGUCGCCGCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ferritin_mouse.fa	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,2 @@
+> mouse ferritin
+CAGACGUUCUCGCCCAGAGUCGCCGCGGUUUCCUGCUUCAACAGUGCUUGAACGGAACCCGGUGCUCGACCCCUCCGACCCCCGCCGGCCGCUUCGAGCCUGAGCCCUUUGCAACUUCGUCGUUCCGCCGCUCCAGCGUCGCCACCGCGCCUCGCCCCGCCGCCACC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-1.aln	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,5 @@
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA
+ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGGCAACUGUCACUCAAUGGGACA
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA
+#A1                ................................................................AAAAAA...................................................................BBB
+#A2                ................................................................123456...................................................................123
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-2.aln	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,3 @@
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1 .............................................................AAAAAA...............................................................................BBB
+#A2 .............................................................123456...............................................................................123
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-c.aln	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,22 @@
+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                ............................................................
+
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA.aln	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,16 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG
+ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU
+
+ACA7               AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+
+ACA7               AUUGGA--AGA---CACU-CUGCG-----ACA
+ACA30              CAACUG--UCA---CUCA-AUGGG-----ACA
+ACA5               GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA59              ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.amprobs	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,108 @@
+64 69 54 59 0.079977
+63 70 53 60 0.0158884
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.bmprobs	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,172 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.epms	Fri Jan 13 16:48:50 2017 -0500
@@ -0,0 +1,4 @@
+epm_id	 score	 structure	 positions
+0	3583	((()))	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 
+