# HG changeset patch
# User rnateam
# Date 1513776894 18000
# Node ID bdb786715d286b65f32908766d26073fc42a3ae0
# Parent  86f517dcfdfba6e40f2a4960ff82f88ff001c902
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29

diff -r 86f517dcfdfb -r bdb786715d28 rnafold.xml
--- a/rnafold.xml	Thu Sep 28 16:24:39 2017 -0400
+++ b/rnafold.xml	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.3">
+<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.4">
     <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
     <macros>
         <token name="@EXECUTABLE@">RNAfold</token>
@@ -31,15 +31,23 @@
     #if $layout_type ==0
         --layout-type=$general_options.layout_type
     #end if
-    #if $mea:
-        --MEA=$mea
+    
+	#if $mea:
+        #if $meagamma:
+            --MEA=$meagamma
+        #else
+            --MEA
+        #end if	 
     #end if
+  
     #if $pf
         $pf
-        #if $pfscale:
-            --pfScale=$pfscale
-        #end if
     #end if
+
+    #if $pfscale:
+        --pfScale=$pfscale
+    #end if
+
     $advancedOptions.noconversion
     $advancedOptions.gquad
     $advancedOptions.nolp
@@ -104,7 +112,7 @@
     #else
         "${input_source.fasta_input}"
     #end if
-    > '$tabular_file'
+    > '$dot_bracket_stdout'
 ]]>
     </command>
 
@@ -132,9 +140,12 @@
             <option value="1" selected="true">Default: Naview layout</option>
             <option value="0">Simple radial layout</option>
         </param>
-        <param argument="--MEA" name="mea" type="float" value="1.0" optional="true" label="Gamma Value" help="Used for the calculation of the Maximum Expected accuracy"/>
+
+        <param name="mea" type="boolean" checked="false" falsevalue="" label="Calculate Maximum Expected accuracy" help="--MEA"/>
+        <param name="meagamma" type="float"  optional="true" label="MEA-Gamma Value"/>
+
         <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
-        <param name="pfscale" type="float" value="1.07" optional="true" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>
+        <param name="pfscale" type="float" optional="true" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>
         <section name="advancedOptions" title="Advanced options">
             <param name="nops" type="boolean" truevalue="--noPS" falsevalue="" checked="false" label="Do not produce postscript drawing of the mfe structure (reduces run-time)" help="(--noPS)"/>
             <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
@@ -279,13 +290,13 @@
         </section>
     </inputs>
     <outputs>
-        <data format="dbn" name="tabular_file"/>
-        <collection name="sequence_outputs" type="list" label="rna_eps outputs">
+        <data format="dbn" name="dot_bracket_stdout"/>
+        <collection name="structure_outputs" type="list" label="rna_strcuture_eps outputs">
             <filter>advancedOptions['nops'] is False</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
         </collection>
-        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
-            <filter>measelect['pf'] is True</filter>
+        <collection name="matrix_outputs" type="list" label="rna_matrix_eps outputs">
+            <filter>pf is True</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
         </collection>
     </outputs>
@@ -293,18 +304,40 @@
         <test>
             <param name="select_fasta" value="true" />
             <param name="fasta_input" value="rnafold_input1.fa"/>
-            <output name="tabular_file" file="rnafold_result1.txt"/>
+            <output name="dot_bracket_stdout" file="rnafold_result1.txt"/>
+        </test>
+        
+        <test>
+            <param name="select_fasta" value="true" />
+            <param name="mea" value="true" />
+            <param name="fasta_input" value="rnafold_input1.fa"/>
+            <output name="dot_bracket_stdout" file="rnafold_result1_mea.txt"/>
         </test>
         <test>
             <param name="select_fasta" value="true" />
+            <param name="pf" value="true" />
+            <param name="fasta_input" value="rnafold_input1.fa"/>
+            <output name="dot_bracket_stdout" file="rnafold_result1_pf.txt"/>
+            <output_collection name="structure_outputs" type="list">
+                <element name="Anolis_caro_chrUn_GL343590.trna2_AlaAGC" file="Anolis_caro_chrUn_GL343590.trna2_AlaAGC_ss.ps"  compare="sim_size" />
+                <element name="Anolis_caro_chrUn_GL343207.trna3_AlaAGC" file="Anolis_caro_chrUn_GL343207.trna3_AlaAGC_ss.ps"  compare="sim_size" />
+            </output_collection>
+            
+            <output_collection name="matrix_outputs" type="list">
+                <element name="Anolis_caro_chrUn_GL343590.trna2_AlaAGC" file="Anolis_caro_chrUn_GL343590.trna2_AlaAGC_dp.ps"  compare="sim_size" />
+                <element name="Anolis_caro_chrUn_GL343207.trna3_AlaAGC" file="Anolis_caro_chrUn_GL343207.trna3_AlaAGC_dp.ps"  compare="sim_size" />
+            </output_collection>
+        </test>       
+        <test>
+            <param name="select_fasta" value="true" />
             <param name="fasta_input" value="rnafold_input2.fa"/>
             <param name="temperature" value="75"/>
-            <output name="tabular_file" file="rnafold_result2.txt"/>
+            <output name="dot_bracket_stdout" file="rnafold_result2.txt"/>
         </test>
         <test>
             <param name="select_fasta" value="false" />
             <param name="input_sequence" value="TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA"/>
-            <output name="tabular_file" file="rnafold_result3.txt"/>
+            <output name="dot_bracket_stdout" file="rnafold_result3.txt"/>
         </test>
         <test>
             <param name="select_fasta" value="true" />
@@ -313,8 +346,9 @@
               <param name="shapeSelector" value="isUsed"/>
             </conditional>
             <param name="shapeFile" value="sample_3.react"/>
-            <output name="tabular_file" file="sample_3_result.txt"/>
+            <output name="dot_bracket_stdout" file="sample_3_result.txt"/>
         </test>
+    
     </tests>
     <help>
 <![CDATA[
diff -r 86f517dcfdfb -r bdb786715d28 test-data/Anolis_caro_chrUn_GL343207.trna3_AlaAGC_dp.ps
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Anolis_caro_chrUn_GL343207.trna3_AlaAGC_dp.ps	Wed Dec 20 08:34:54 2017 -0500
@@ -0,0 +1,370 @@
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diff -r 86f517dcfdfb -r bdb786715d28 test-data/Anolis_caro_chrUn_GL343207.trna3_AlaAGC_ss.ps
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Anolis_caro_chrUn_GL343207.trna3_AlaAGC_ss.ps	Wed Dec 20 08:34:54 2017 -0500
@@ -0,0 +1,231 @@
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diff -r 86f517dcfdfb -r bdb786715d28 test-data/Anolis_caro_chrUn_GL343590.trna2_AlaAGC_dp.ps
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Anolis_caro_chrUn_GL343590.trna2_AlaAGC_dp.ps	Wed Dec 20 08:34:54 2017 -0500
@@ -0,0 +1,507 @@
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diff -r 86f517dcfdfb -r bdb786715d28 test-data/Anolis_caro_chrUn_GL343590.trna2_AlaAGC_ss.ps
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Anolis_caro_chrUn_GL343590.trna2_AlaAGC_ss.ps	Wed Dec 20 08:34:54 2017 -0500
@@ -0,0 +1,230 @@
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+  % puts optimal x1 y1 x2 y2 coordinates used in bezier curves from i to j
+  % onto the stack
+  dup 3 -1 roll dup 4 -1 roll lt dup dup 5 2 roll {exch} if
+  dup 3 -1 roll dup 3 -1 roll exch sub 1 sub dup
+  4 -2 roll 5 -1 roll {exch} if 4 2 roll
+  sequence length dup 2 div exch 3 1 roll lt 
+  {exch 5 -1 roll pop 4 -2 roll exch 4 2 roll}
+  { 4 2 roll 5 -1 roll dup 6 1 roll {exch} if
+    4 -2 roll exch pop dup 3 -1 roll dup 4 1 roll
+    exch add 4 -1 roll dup 5 1 roll sub 1 sub
+    5 -1 roll not {4 -2 roll exch 4 2 roll} if
+  }ifelse
+   % compute the scalingfactor and prepare (1-sf) and sf*r
+  2 mul exch cpr 3 1 roll div dup
+  3 -1 roll mul exch 1 exch sub exch
+   % compute the coordinates
+  3 -1 roll 1 sub coor exch get aload pop % get coord for i
+  4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate y1
+  4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate x1
+  5 -1 roll 1 sub coor exch get aload pop % get coord for j
+  % duplicate j coord
+  dup 3 -1 roll dup 4 1 roll exch 8 2 roll
+  6 -1 roll dup 7 1 roll mul 5 -1 roll dup 6 1 roll add exch % calculate y2
+  6 -1 roll mul 5 -1 roll add exch % calculate x2
+  6 -2 roll % reorder
+} bind def
+/drawoutline {
+  gsave outlinecolor newpath
+  coor 0 get aload pop 0.8 0 360 arc % draw 5' circle of 1st sequence
+  currentdict /cutpoint known        % check if cutpoint is defined
+  {coor 0 cutpoint getinterval
+   {aload pop lineto} forall         % draw outline of 1st sequence
+   coor cutpoint 1 add get aload pop
+   2 copy moveto 0.8 0 360 arc       % draw 5' circle of 2nd sequence
+   coor cutpoint 1 add coor length cutpoint 1 add sub getinterval
+   {aload pop lineto} forall}        % draw outline of 2nd sequence
+  {coor {aload pop lineto} forall}   % draw outline as a whole
+  ifelse
+  stroke grestore
+} bind def
+/drawpairs {
+  paircolor
+  0.7 setlinewidth
+  [9 3.01] 9 setdash
+  newpath
+  pairs {aload pop
+      currentdict (cpr) known
+      { exch dup
+        coor  exch 1 sub get aload pop moveto
+        exch arccoords curveto
+      }
+      { coor exch 1 sub get aload pop moveto
+        coor exch 1 sub get aload pop lineto
+      }ifelse
+  } forall
+  stroke
+} bind def
+% draw bases
+/drawbases {
+  [] 0 setdash
+  seqcolor
+  0
+  coor {
+    aload pop moveto
+    dup sequence exch 1 getinterval cshow
+    1 add
+  } forall
+  pop
+} bind def
+
+/init {
+  /Helvetica findfont fsize scalefont setfont
+  1 setlinejoin
+  1 setlinecap
+  0.8 setlinewidth
+  72 216 translate
+  % find the coordinate range
+  /xmax -1000 def /xmin 10000 def
+  /ymax -1000 def /ymin 10000 def
+  coor {
+      aload pop
+      dup ymin lt {dup /ymin exch def} if
+      dup ymax gt {/ymax exch def} {pop} ifelse
+      dup xmin lt {dup /xmin exch def} if
+      dup xmax gt {/xmax exch def} {pop} ifelse
+  } forall
+  /size {xmax xmin sub ymax ymin sub max} bind def
+  72 6 mul size div dup scale
+  size xmin sub xmax sub 2 div size ymin sub ymax sub 2 div
+  translate
+} bind def
+end
+%%EndProlog
+RNAplot begin
+% data start here
+/sequence (\
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA\
+) def
+/coor [
+[102.34599304 225.12051392]
+[110.41094971 210.84155273]
+[109.77433014 195.85507202]
+[109.13771057 180.86859131]
+[108.50109100 165.88211060]
+[107.86447144 150.89561462]
+[107.22785950 135.90913391]
+[90.28739166 133.48460388]
+[77.11851501 123.91786957]
+[70.32070923 110.05319977]
+[55.37474823 111.32528687]
+[40.42878342 112.59737396]
+[25.48282242 113.86946106]
+[17.57515907 127.22043610]
+[3.31690264 133.34266663]
+[-11.80935574 129.88204956]
+[-21.98726082 118.16923523]
+[-23.30319977 102.70806122]
+[-15.25116920 89.44365692]
+[-0.92733771 83.47645569]
+[14.16048908 87.10096741]
+[24.21073341 98.92350006]
+[39.15669632 97.65141296]
+[54.10265732 96.37932587]
+[69.04862213 95.10723114]
+[75.20735168 80.83619690]
+[87.46604156 71.28019714]
+[84.93103027 56.49596024]
+[82.39601898 41.71172333]
+[79.86100006 26.92748451]
+[77.32598877 12.14324570]
+[63.73017883 4.41744947]
+[58.32971573 -10.25800610]
+[63.67453384 -24.95381927]
+[77.24097443 -32.73107910]
+[92.62337494 -29.91759682]
+[102.55863953 -17.84181786]
+[102.35564423 -2.20555139]
+[92.11022949 9.60823345]
+[94.64524078 24.39247131]
+[97.18025208 39.17671204]
+[99.71526337 53.96094894]
+[102.25028229 68.74518585]
+[111.61898041 69.95008087]
+[120.45154572 73.97383881]
+[127.89853668 80.59681702]
+[133.19635010 89.34370422]
+[135.74378967 99.51597595]
+[135.16680908 110.24712372]
+[150.04531860 112.15238953]
+[164.92382812 114.05766296]
+[179.80232239 115.96292877]
+[194.68083191 117.86819458]
+[206.04914856 107.13062286]
+[221.66270447 106.26418304]
+[234.14927673 115.67798615]
+[237.61306763 130.92712402]
+[230.41859436 144.81141663]
+[215.96286011 150.77513123]
+[201.07142639 146.00236511]
+[192.77557373 132.74670410]
+[177.89706421 130.84143066]
+[163.01855469 128.93617249]
+[148.14004517 127.03089905]
+[133.26153564 125.12563324]
+[122.21434021 135.27252197]
+[122.85095978 150.25900269]
+[123.48757935 165.24548340]
+[124.12419128 180.23197937]
+[124.76081085 195.21846008]
+[125.39743042 210.20494080]
+[134.64427185 223.74850464]
+[127.29573059 238.40902710]
+] def
+/pairs [
+[2 71]
+[3 70]
+[4 69]
+[5 68]
+[6 67]
+[7 66]
+[10 25]
+[11 24]
+[12 23]
+[13 22]
+[27 43]
+[28 42]
+[29 41]
+[30 40]
+[31 39]
+[49 65]
+[50 64]
+[51 63]
+[52 62]
+[53 61]
+] def
+
+init
+
+% switch off outline pairs or bases by removing these lines
+drawoutline
+drawpairs
+drawbases
+% show it
+showpage
+end
+%%EOF
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaalifold_input1.fa
--- a/test-data/rnaalifold_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaalifold_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL34
+>Anolis_caro_chrUn_GL34
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL35
+>Anolis_caro_chrUn_GL35
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaduplex_input1.fa
--- a/test-data/rnaduplex_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaduplex_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaduplex_result1.txt
--- a/test-data/rnaduplex_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaduplex_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,3 +1,3 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC
 .((((((..((......((((...((((..(((.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..))))))..)))..)))).......)))).)))))))).   1,73  :   1,72  (-40.70)
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnafold_input1.fa
--- a/test-data/rnafold_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnafold_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2_AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3_AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnafold_input2.fa
--- a/test-data/rnafold_input2.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnafold_input2.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnafold_result1.txt
--- a/test-data/rnafold_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnafold_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,14 +1,6 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-A
+>Anolis_caro_chrUn_GL343590.trna2_AlaAGC
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 .((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
-,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)), [-23.20]
-.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 d=9.72}
-.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 MEA=58.88}
- frequency of mfe structure in ensemble 0.142309; ensemble diversity 14.51 
->Anolis_carolinensis_chrUn_GL343207.trna3-A
+>Anolis_caro_chrUn_GL343207.trna3_AlaAGC
 GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
 (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-29.60)
-(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). [-29.88]
-(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 d=0.64}
-(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 MEA=71.81}
- frequency of mfe structure in ensemble 0.63265; ensemble diversity 1.15  
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnafold_result1_mea.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result1_mea.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -0,0 +1,14 @@
+>Anolis_caro_chrUn_GL343590.trna2_AlaAGC
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
+,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)), [-23.20]
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 d=9.72}
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 MEA=58.88}
+ frequency of mfe structure in ensemble 0.142309; ensemble diversity 14.51 
+>Anolis_caro_chrUn_GL343207.trna3_AlaAGC
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-29.60)
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). [-29.88]
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 d=0.64}
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 MEA=71.81}
+ frequency of mfe structure in ensemble 0.63265; ensemble diversity 1.15  
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnafold_result1_pf.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result1_pf.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -0,0 +1,12 @@
+>Anolis_caro_chrUn_GL343590.trna2_AlaAGC
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
+,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)), [-23.20]
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 d=9.72}
+ frequency of mfe structure in ensemble 0.142309; ensemble diversity 14.51 
+>Anolis_caro_chrUn_GL343207.trna3_AlaAGC
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-29.60)
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). [-29.88]
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 d=0.64}
+ frequency of mfe structure in ensemble 0.63265; ensemble diversity 1.15  
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnafold_result2.txt
--- a/test-data/rnafold_result2.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnafold_result2.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,14 +1,6 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-A
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 ..(((.....((((....((..(((....)))..))...)))).....(((((.......)))))....))). ( -3.37)
-.{((,..,..{(({.,{,.{,.(((....)))},.}},.}}}},,..,(((((.......)))))..,,})). [ -7.81]
-...........((...(.....(((....)))....)...))......(((((.......)))))........ {  2.85 d=11.83}
-.((........(((..(.....(((....)))....)..)))......(((((.......))))).....)). {  1.96 MEA=51.92}
- frequency of mfe structure in ensemble 0.00162209; ensemble diversity 17.27 
->Anolis_carolinensis_chrUn_GL343207.trna3-A
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC
 GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
 (((((..((.(((.....((..(((....)))..))......))).))(((((.......)))))..))))). ( -5.02)
-(((((..,..{({...{,.{.,{((....))),..},,..,.}},.,,(((((.......))))).,))))). [ -9.30]
-(((((.................(((....)))................(((((.......)))))..))))). { -4.42 d=10.17}
-(((((......((.........(((....)))..........))....(((((.......)))))..))))). { -2.50 MEA=54.73}
- frequency of mfe structure in ensemble 0.00205781; ensemble diversity 15.91 
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnafold_result3.txt
--- a/test-data/rnafold_result3.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnafold_result3.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,7 +1,3 @@
 >Sequence
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 .((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
-,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)), [-23.20]
-.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 d=9.72}
-.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 MEA=58.88}
- frequency of mfe structure in ensemble 0.142309; ensemble diversity 14.51 
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnalfold_input1.fa
--- a/test-data/rnalfold_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnalfold_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnalfold_result1.txt
--- a/test-data/rnalfold_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnalfold_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 .((((....)))).	( -0.10)	56
 .(((..((((....)))).))).	( -3.40)	51
 .(((((.......))))).	( -7.70)	48
@@ -13,7 +13,7 @@
 .((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).	(-22.00)	1
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
  (-22.00)
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 .(((..((((....)))).))).	( -3.40)	51
 .(((((.......))))).	( -9.20)	48
 .((((..(((((.......)))))..)))).	(-11.80)	42
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnapaln_input1.fa
--- a/test-data/rnapaln_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnapaln_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnapaln_result1.txt
--- a/test-data/rnapaln_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnapaln_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,5 +1,5 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 68.8844
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 ,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)),
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnapdist_input1.fa
--- a/test-data/rnapdist_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnapdist_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnapdist_result1.txt
--- a/test-data/rnapdist_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnapdist_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,3 +1,3 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 8.66253
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnapkplex_input1.fa
--- a/test-data/rnapkplex_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnapkplex_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnapkplex_result1.txt
--- a/test-data/rnapkplex_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnapkplex_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,6 +1,6 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 .((((((..((((........)))).(((((.......))))).[[[.(((((]]]....))))))))))).. (-31.90)
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
 (((((((..((((..[[[.[[)))).(((((.]].]]]))))).....(((((.......)))))))))))). (-38.54)
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaplex_input1.fa
--- a/test-data/rnaplex_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaplex_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaplex_result1.txt
--- a/test-data/rnaplex_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaplex_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 .((((((..((......((((...((((..(((.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..))))))..)))..)))).......)))).)))))))).   1,73  :   1,72  (-40.70) i:72,j:1 <-41.26>
 
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaplfold_input1.fa
--- a/test-data/rnaplfold_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaplfold_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-A (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-A (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaplot_input1.fa
--- a/test-data/rnaplot_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaplot_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnasubopt_input1.fa
--- a/test-data/rnasubopt_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnasubopt_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnasubopt_result1.txt
--- a/test-data/rnasubopt_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnasubopt_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,7 +1,7 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-A [0]
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC [0]
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA -22.00   0.00
 (((((((..((((........)))).(((((.......))))).....(((((.......))))))))).))) -22.00
 .((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. -22.00
->Anolis_carolinensis_chrUn_GL343207.trna3-A [0]
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC [0]
 GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA -29.60   0.00
 (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). -29.60
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaup_input1.fa
--- a/test-data/rnaup_input1.fa	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaup_input1.fa	Wed Dec 20 08:34:54 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 86f517dcfdfb -r bdb786715d28 test-data/rnaup_result1.txt
--- a/test-data/rnaup_result1.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/rnaup_result1.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,6 +1,6 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC
   55,  58 	 (0.019) 	 for u=  4
-RNAup output in file: Anolis_carolinensis_chrUn_GL343590.trna2-A_u1.out
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC
+RNAup output in file: Anolis_caro_chrUn_GL343590.trna2-AlaAGC_u1.out
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC
   16,  19 	 (0.004) 	 for u=  4
-RNAup output in file: Anolis_carolinensis_chrUn_GL343207.trna3-A_u1.out
+RNAup output in file: Anolis_caro_chrUn_GL343207.trna3-AlaAGC_u1.out
diff -r 86f517dcfdfb -r bdb786715d28 test-data/sample_3_result.txt
--- a/test-data/sample_3_result.txt	Thu Sep 28 16:24:39 2017 -0400
+++ b/test-data/sample_3_result.txt	Wed Dec 20 08:34:54 2017 -0500
@@ -1,21 +1,9 @@
 >SECIS_1
 AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
 .((((...(((.(..(((.((((((((........))))))))))).).))).....)))).. (-27.97)
-.((((...(((.{..(((.((((((((........))))))))))).}.))).....)))}.. [-29.13]
-..(((...(((....(((.((((((((........)))))))))))...))).....)))... {-26.59 d=5.82}
-.((((...(((.(..(((.((((((((........))))))))))).).))).....)))).. {-27.97 MEA=54.87}
- frequency of mfe structure in ensemble 0.151171; ensemble diversity 8.50
 >6S_1
 GAAACCCUAAUGUAUUCGAUAUAGUUCCUGAUAUUUUUGAACCGAACAAUUUUUUAUACCUAGGGAGCUUGGAGUUCCGGCGCGGCGCACAUGCCUUCACACGAGGAAGUGCAAACCGUUAGACAGAGCACCCACCUGCUUUAAUUGAGAGCGGGUUCAAAGGAAGGGAAUCCUAAACGGUACGAUUGGGGUUUCU
 (((((((...(((((.((.....((((((....((((((((((...................(((.((((.....((.((((.(..((((.(.((((.....))))).))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))))......)))))))....))))))). (-110.38)
-(((((((,,{(((((,((.....{(((((....(((((((((({{{....,},.........(((.((((.....((.((((.(..((((.{.((((.....)))),.))))...))))).))}.)))).)))....(((((.....))))).))))))))))..))))),......))))))).}.,))))))). [-115.12]
-(((((((..((((((.((......(((((....((((((((((...................(((.((((.....((.((((.(..((((...((((.....))))..))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))).......))))))).)..))))))). {-109.37 d=10.73}
-(((((((..((((((.((......(((((....((((((((((...................(((.((((.....((.((((.(..((((...((((.....))))..))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))).......))))))).)..))))))). {-109.37 MEA=177.59}
- frequency of mfe structure in ensemble 0.000456946; ensemble diversity 17.02
 >6S_2
 UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
 .((.(((((((((((.(((.(...((((...((.((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............))))))))))))..)))).).))))))).))))))))).. (-129.27)
-.((,(((((((((((.(((.{...((((...,,.((((.((((((..(((....))).....((((((((...{(.(((((.((.((..((((((,....,))))))))))...))))).)}..)))))))).....,,...,,.)))))))))),}..)))).}.))))))).))))))))).. [-132.48]
-.((.(((((((((((.(((.(...((((......((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............))))))))))....)))).).))))))).))))))))).. {-129.23 d=10.34}
-.((.(((((((((((.(((.(...((((...(..((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............)))))))))).)..)))).).))))))).))))))))).. {-128.23 MEA=168.16}
- frequency of mfe structure in ensemble 0.00547171; ensemble diversity 14.91