changeset 0:c05c83b3ef0f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster commit 4406735e44aba20859c252be39f4e99df28c7a92
author rnateam
date Sat, 27 Oct 2018 13:21:39 -0400
parents
children 953353eacec2
files align_cluster.xml hg38.100way.nh hg38.20way.nh test-data/alignment1.clustal test-data/alignment1.cons.tsv test-data/alignment1.evofold.out test-data/alignment1.png test-data/alignment1.ps test-data/alignment1.rnaz.out test-data/alignment1.sth test-data/alignment1_R2R.sto.pdf test-data/alignment2.clustal test-data/alignment2.cons.tsv test-data/alignment2.evofold.out test-data/alignment2.png test-data/alignment2.rnaz.out test-data/alignment2.sth test-data/alignment2b-transcript.fa test-data/alignment2b.cons.tsv test-data/cluster1.all test-data/cluster1.all.fa test-data/cluster2.all test-data/cluster2.all.fa test-data/structure.png test-data/structure.ps test-data/structure1.png test-data/structure1.ps test-data/structure2.png
diffstat 25 files changed, 1791 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align_cluster.xml	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,224 @@
+<tool id="graphclust_align_cluster" name="Align GraphClust cluster " version="0.1" >
+<description>structural alignment and conservation analysis of predicted clusters</description> 
+  <requirements>
+      <requirement type="package" version="0.6.0">graphclust-wrappers</requirement>
+      <requirement type="package" version='0.5'>perl-array-utils</requirement>
+      <requirement type="package" version='0.18.1'>scikit-learn</requirement>
+      <requirement type="package" version='1.8.10'>locarna</requirement>
+      <requirement type="package" version='2.1'>rnaz</requirement>
+      <requirement type="package" version="1.1.2">infernal</requirement>
+      <requirement type="package" version='2.2.10'>viennarna</requirement>
+      <requirement type="package" version='1.3.30'>graphicsmagick</requirement>
+      <requirement type="package" version='0.6.1'>rscape</requirement>
+      <requirement type="package" version='6.0'>unzip</requirement>
+      <requirement type="package" version='0.1'>evofold2</requirement>
+      <requirement type="package" version='1.70'>biopython</requirement>
+      <requirement type="package" version='0.23.0'>pandas</requirement>
+  </requirements>
+  <command detect_errors="aggressive">
+  <![CDATA[
+      #set $alignment_clustal = 'cluster.aln'
+      mkdir ./RESULTS/ &&
+      'gc_align_clusters.pl'
+      '$cluster_all_fa'
+      ./RESULTS/ C1 
+      $results_top_num
+
+      "
+        #if  str($advanced_opts.advanced_opts_selector) == "show":
+            #if  str($advanced_opts.param_type.param_type_selector) == "gclust":
+                  $advanced_opts.param_type.p
+                  $advanced_opts.param_type.max_diff_am
+                  $advanced_opts.param_type.max_diff
+                  $advanced_opts.param_type.tau
+                  $advanced_opts.param_type.struct_weight
+                  $advanced_opts.param_type.indel_opening
+                  $advanced_opts.param_type.indel
+                  $advanced_opts.param_type.alifold_consensus_dp
+            #end if
+        #end if
+      "
+      && 
+      R-scape --outdir ./RESULTS/ result.aln.sth &&
+      RNAz --locarnate '$alignment_clustal' > alignment.rnaz.out &&
+      #if  str($genomic_cons_opts.genomic_cons_opts_selector) != "no":
+          clustal_to_alma.py '$alignment_clustal' $cluster_all &&
+          EvoFoldV2.sh -o alignment.evofold.out '${alignment_clustal}.ama'
+          #if  str($genomic_cons_opts.genomic_cons_opts_selector) == "hg38_100way":
+             '$__tool_directory__/hg38.100way.nh'
+          #elif str($genomic_cons_opts.genomic_cons_opts_selector) == "hg38_20way":
+             '$__tool_directory__/hg38.20way.nh'
+          #else 
+         '$alignment_clustal'.ama '$genomic_cons_opts.phylo_tree'
+      #end if
+      &&
+    #else
+      touch alignment.evofold.out &&
+    #end if
+    
+    extract_conservation_metrics.py 
+    '$alignment_clustal' alignment.rnaz.out RESULTS/result.aln.sum alignment.evofold.out  
+    '$cluster_all' 
+    #if  str($bed_opts.bed_opts_selector) == "yes":
+        '$bed_opts.transcript_loci_fasta' 
+    '$bed_opts.transcript_loci_bed' 
+    '$bed_opts.genome_version' 
+  #else  
+    '' '' ''
+  #end if
+  conservation_metrics.tsv
+   
+]]>
+  </command>
+  <inputs>
+      <param type="data" name="cluster_all_fa" label="cluster-sequences-sorted" format="fasta"
+        help="Cluster sequences from the collect-result step"/>
+      <param type="data" name="cluster_all" label="cmsearch-results" format="txt"
+        help="Tabular cmsearch results of the cluster-collection step (CLUSTERS-cmsearch)"/>
+      <param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" 
+        help="Top number of cmsearch hit sequences are used for structural alignment and metrics"/>
+
+      <conditional name="genomic_cons_opts">
+          <param type="select" name="genomic_cons_opts_selector" label="Phylo tree for evofold" 
+              help="For MAF genomic alignments as input data, corresponding phylo tree is required to perform Evofold2 structural conservation predcition. For other genomic alignemnts, please upload the tree file.">
+              <option value="no">No</option>
+              <option value="hg38_100way">hg38-100way</option>
+              <option value="hg38_20way">hg38-20way</option>
+              <option value="user_phylo_tree">from history</option>
+          </param>
+          <when value="no" />
+          <when value="hg38_100way" />
+          <when value="hg38_20way" />                
+          <when value="user_phylo_tree">
+              <param format="newick" name="phylo_tree" type="data" label="Newick phylo-tree" />
+          </when>
+      </conditional>
+      <conditional name="bed_opts">
+          <param type="select" name="bed_opts_selector" label="Extract genomic coordinates of the clusters" >
+              <option value="no">No</option>
+              <option value="yes">Yes</option>
+          </param>
+          <when value="no" />
+          <when value="yes" >
+              <param format="fasta" name="transcript_loci_fasta" type="data" label="Loci reference sequence"
+                help="Sequence of reference species (human) for the genomic loci (precursor mRNA/lncRNA) to locate the clusters" />
+              <param name='transcript_loci_bed' type="text" value="chr1 0 100000 gene 0 +" 
+                help="bed entry string of the reference transcript loci for bed/ucsc-track output. 'chrom start end name score strand' white-space separated.">
+                <validator type="regex" message="one-line bed string must have at least 6 entries as BED6 format (chrom start end name 0 strand) 
+                (space and tab allowed)">^\S+\s+[0-9]+\s+[0-9]+\s+\S+\s+\S+\s+[-+]\s*$</validator> 
+              </param>
+              <param name='genome_version' value="hg38" type="text" label="reference genome assembly"
+                help="ucsc reference genome assembly version used in the input MAF alignments (e.g. hg38, hg19, mm10). To identify the reference in clusters">
+                  <validator type="regex" message="ucsc genome assembly version has an alphabet prefix and a number suffix">^[a-zA-Z]+[0-9]+$</validator> 
+              </param>
+          </when>
+      </conditional> 
+      <conditional name="advanced_opts">
+          <param name="advanced_opts_selector" type="select" label="Locarna alignment options">
+              <option value="hide" selected="True">Hide</option>
+              <option value="show">Show</option>
+          </param>
+          <when value="hide"></when>
+          <when value="show">
+              <conditional name="param_type">
+                  <param name="param_type_selector" type="select" label="Choose the type of parameters">
+                      <option value="locarna">LocARNA defaults</option>
+                      <option value="gclust" selected="True">GrapClust defaults(changeable)</option>
+                  </param>
+                  <when value="gclust">
+                      <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
+                      <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>
+                      <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>
+                      <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
+                      <param name="struct_weight" argument="struct-weight"
+                              label="Structure weight" type="integer"
+                              value="180" min="0" max="800" />
+                       <param name="indel_opening" argument="indel-opening"
+                              label="Indel opening score" type="integer"
+                              value="-400" max="0" min="-1500" />
+                       <param argument="indel" label="Indel score" type="integer"
+                              value="-200" min="-1000" max="0" />
+                       <param  name="alifold_consensus_dp"
+                               type="boolean" checked="True"
+                               truevalue="--alifold-consensus-dp" falsevalue=" "
+                               label="Compute consensus dot plot by alifold" />
+                  </when>
+                  <when value="locarna">
+                  </when>
+              </conditional>
+          </when>
+      </conditional>
+  </inputs>
+  <outputs>
+      <data name="alignment_ps" format="data" from_work_dir="cluster.aln.ps" label="alignment.ps"  />
+      <data name="alignment_png" format="png" from_work_dir="cluster.aln.png" label="alignment.png"  />
+      <data name="structure_ps" format="data" from_work_dir="cluster.alirna.ps" label="structure.ps"  />
+      <data name="structure_png" format="png" from_work_dir="cluster.alirna.png" label="structure.png"  /> 
+      <data name="alignment_sth" format="stockholm" from_work_dir="result.aln.sth" label="alignment.sth"  />
+      <data name="alignment_clustal_out" format="clustal" from_work_dir="cluster.aln" label="alignment.clustal"  />
+      <data name="Rscape_R2R" format="pdf" from_work_dir="RESULTS/result.aln_1.R2R.sto.pdf" label="Rscape-R2R"  />
+      <data name="rnaz_out" format="txt" from_work_dir="alignment.rnaz.out" label="rnaz.out"  />
+      <data name="rscape_out" format="txt" from_work_dir="alignment.sum" label="Rscape.summary"  />
+      <data name="evofold_out" format="txt" from_work_dir="alignment.evofold.out" label="evofold.out"  />
+      <data name="cons_tsv" format="tabular" from_work_dir="conservation_metrics.tsv" label="conservation_metrics.tsv"  />    
+  </outputs>
+  <tests>
+        <test>
+            <param name="cluster_all_fa" value="cluster1.all.fa"/>
+            <param name="cluster_all" value="cluster1.all"/>
+            <output name="alignment_ps" file="alignment1.ps" compare="sim_size" />
+            <output name="alignment_png" file="alignment1.png" compare="sim_size" />
+            <output name="structure_ps" file="structure1.ps" compare="sim_size" />
+            <output name="structure_png" file="structure1.png" compare="sim_size" /> 
+            <output name="alignment_sth" file="alignment1.sth"  compare="sim_size" delta="100" />
+            <output name="alignment_clustal_out" file="alignment1.clustal" />
+            <output name="Rscape_R2R" file="alignment1_R2R.sto.pdf" compare="sim_size" />
+            <output name="rnaz_out" file="alignment1.rnaz.out"  compare="sim_size" delta="10"/>
+            <output name="evofold_out" file="alignment1.evofold.out"  />
+            <output name="cons_tsv" file="alignment1.cons.tsv"   compare="sim_size" delta="0"/>
+            <conditional name="genomic_cons_opts">
+                <param name="genomic_cons_opts_selector" value="no"/>
+            </conditional>
+            <param name="results_top_num" value="5"/>
+
+        </test>
+        
+        <test>
+            <param name="cluster_all_fa" value="cluster2.all.fa"/>
+            <param name="cluster_all" value="cluster2.all"/>
+            <output name="alignment_png" file="alignment2.png" compare="sim_size" />
+            <output name="structure_png" file="structure2.png" compare="sim_size" /> 
+            <output name="alignment_sth" file="alignment2.sth"  compare="sim_size" delta="100" />
+            <output name="alignment_clustal_out" file="alignment2.clustal" />
+            <output name="rnaz_out" file="alignment2.rnaz.out"  />
+            <output name="evofold_out" file="alignment2.evofold.out"  />
+            <output name="cons_tsv" file="alignment2.cons.tsv"  />
+            <conditional name="genomic_cons_opts">
+                <param name="genomic_cons_opts_selector" value="hg38_20way"/>
+            </conditional>
+        </test>  
+
+        <test>
+            <param name="cluster_all_fa" value="cluster2.all.fa"/>
+            <param name="cluster_all" value="cluster2.all"/>
+            <output name="cons_tsv" file="alignment2b.cons.tsv"  />
+            <conditional name="genomic_cons_opts">
+                <param name="genomic_cons_opts_selector" value="hg38_20way"/>
+            </conditional>
+            <conditional name="bed_opts">
+                <param name="bed_opts_selector" value="yes"/>
+                <param name="transcript_loci_fasta" value="alignment2b-transcript.fa"/>
+                <param name="transcript_loci_bed" value="chr7 27162434 27166719 Hoxa9-Xtend5UTR 2 -"/>
+            </conditional>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+        Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations. 
+
+    ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.5281/zenodo.597695</citation>
+  </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hg38.100way.nh	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,100 @@
+((((((((((((((((((hg38:0.00655,
+                 panTro4:0.00684):0.00422,
+                gorGor3:0.008964):0.009693,
+               ponAbe2:0.01894):0.003471,
+              nomLeu3:0.02227):0.01204,
+             (((rheMac3:0.004991,
+               macFas5:0.004991):0.003,
+              papAnu2:0.008042):0.01061,
+             chlSab2:0.027000):0.025000):0.021830,
+            (calJac3:0.03,
+            saiBol1:0.010350):0.019650):0.072610,
+           otoGar3:0.13992):0.013494,
+          tupChi1:0.174937):0.002,
+         (((speTri2:0.125468,
+           (jacJac1:0.1,
+           ((micOch1:0.08,
+            (criGri1:0.04,
+            mesAur1:0.040000):0.040000):0.060000,
+           (mm10:0.084509,
+           rn6:0.091589):0.047773):0.060150):0.100000):0.022992,
+          (hetGla2:0.1,
+          (cavPor3:0.065629,
+          (chiLan1:0.06,
+          octDeg1:0.100000):0.060000):0.050000):0.060150):0.025746,
+         (oryCun2:0.114227,
+         ochPri3:0.201069):0.101463):0.015313):0.020593,
+        (((susScr3:0.12,
+          ((vicPac2:0.047275,
+           camFer1:0.04):0.04,
+          ((turTru2:0.034688,
+           orcOrc1:0.039688):0.03,
+          (panHod1:0.1,
+          (bosTau8:0.1,
+          (oviAri3:0.05,
+          capHir1:0.050000):0.050000):0.010000):0.013592):0.025153):0.020335):0.020000,
+         (((equCab2:0.059397,
+           cerSim1:0.025):0.05,
+          (felCat8:0.098612,
+          (canFam3:0.052458,
+          (musFur1:0.05,
+          (ailMel1:0.02,
+          (odoRosDiv1:0.02,
+          lepWed1:0.020000):0.020000):0.030000):0.030000):0.020000):0.049845):0.006219,
+         ((pteAle1:0.05,
+          pteVam1:0.063399):0.05,
+         (eptFus1:0.02,
+         (myoDav1:0.04,
+         myoLuc2:0.042540):0.050000):0.060000):0.033706):0.004508):0.011671,
+        (eriEur2:0.221785,
+        (sorAra2:0.169562,
+        conCri1:0.100000):0.100000):0.056393):0.021227):0.023664,
+       (((((loxAfr3:0.002242,
+           eleEdw1:0.05):0.04699,
+          triMan1:0.1):0.049697,
+         (chrAsi1:0.03,
+         echTel2:0.235936):0.010000):0.030000,
+        oryAfe1:0.03):0.02,
+       dasNov3:0.169809):0.006717):0.234728,
+      (monDom5:0.125686,
+      (sarHar1:0.1,
+      macEug2:0.072008):0.050000):0.215100):0.071664,
+     ornAna1:0.456592):0.109504,
+    (((((colLiv1:0.1,
+        ((falChe1:0.1,
+         falPer1:0.1):0.03,
+        (((ficAlb2:0.04,
+          ((zonAlb1:0.034457,
+           geoFor1:0.041261):0.015,
+          taeGut2:0.060000):0.010000):0.052066,
+         pseHum1:0.06):0.025,
+        (melUnd1:0.046985,
+        (amaVit1:0.026,
+        araMac1:0.026000):0.010000):0.040000):0.064703):0.060000):0.050000,
+       (anaPla1:0.1,
+       (galGal4:0.041254,
+       melGal1:0.085718):0.031045):0.090000):0.220000,
+      allMis1:0.25):0.045143,
+     ((cheMyd1:0.1,
+      chrPic2:0.1):0.05,
+     (pelSin1:0.1,
+     apaSpi1:0.100000):0.050000):0.040000):0.010000,
+    anoCar2:0.447000):0.122000):0.050000,
+   xenTro7:0.977944):0.1,
+  latCha1:0.977944):0.111354,
+ (((((((tetNig2:0.124159,
+       (fr3:0.103847,
+       takFla1:0.100000):0.100000):0.097590,
+      (oreNil2:0.1,
+      (neoBri1:0.05,
+      (hapBur1:0.05,
+      (mayZeb1:0.05,
+      punNye1:0.050000):0.050000):0.050000):0.100000):0.100000):0.097590,
+     (oryLat2:0.38197,
+     xipMac1:0.400000):0.100000):0.015000,
+    gasAcu1:0.246413):0.045,
+   gadMor1:0.25):0.22564,
+  (danRer10:0.430752,
+  astMex1:0.400000):0.300000):0.143632,
+ lepOcu1:0.400000):0.326688):0.200000,
+petMar2:0.975747);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hg38.20way.nh	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,20 @@
+((((((((((((hg38:0.00988692,
+           panTro4:0.00346722):0.00188147,
+          panPan1:0.00264326):0.00531373,
+         gorGor3:0.00893149):0.00925601,
+        ponAbe2:0.0188981):0.0034213,
+       nomLeu3:0.0230926):0.011557,
+      ((((rheMac3:0.00340845,
+         macFas5:0.00235962):0.00535291,
+        papAnu2:0.00850951):0.0040808,
+       chlSab2:0.0129507):0.00594416,
+      (nasLar1:0.00691583,
+      rhiRox1:0.00647931):0.0119022):0.0216071):0.0217539,
+     (calJac3:0.0352577,
+     saiBol1:0.0327629):0.0373501):0.0612174,
+    tarSyr2:0.142005):0.0118853,
+   (micMur1:0.092909,
+   otoGar3:0.128695):0.0342627):0.0166216,
+  tupBel1:0.184214):0.0152928,
+ mm10:0.330771):0.0876596,
+canFam3:0.0876596);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment1.clustal	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,9 @@
+CLUSTAL W --- LocARNA 1.8.10
+
+
+
+SEQ47_2_50_+       AGGUAU-UAGAAAAAC-CAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC
+SEQ42_1_50_+       GUAAAUAUAGUUUAAC-CAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC
+SEQ41_1_50_+       ACUCUUUUAGUAUAAA-UAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC
+SEQ39_1_50_+       GUUCUUGUAGUUGAAA-UACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU
+SEQ34_1_51_+       CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment1.cons.tsv	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,2 @@
+	Background model	Columns	Combinations/Pair	Consensus MFE	Covariance contribution	Decision model	Energy contribution	G+C content	Mean pairwise identity	Mean single sequence MFE	Mean z-score	Prediction	Reading direction	SVM RNA-class probability	SVM decision value	Sequences	Shannon entropy	Structure conservation index	alignment	multihit per_species	num_human_seqs_all	num_seqs	num_seqs_all	rscape_#target_E-val	rscape_Found	rscape_MSA	rscape_PPV	rscape_SEN	rscape_TP	rscape_True	rscape_alen	rscape_avgid	rscape_method	rscape_nseq	rscape_out	cluster_bed	cluster_human_ids	cluster_human_loc
+0	dinucleotide	51	2.890	-7.640	-4.520	structural RNA alignment quality	-3.120	0.320	44.050	-5.080	0.220	RNA	forward	1.000	3.530	5.000	1.035	1.500	cluster.aln	0	0	5	12	0.050	5	result.aln_1	100.000	55.560	5	9	50	44.730	GTp	5	RESULTS/result.aln.sum			
Binary file test-data/alignment1.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment1.ps	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,184 @@
+%!PS-Adobe-3.0 EPSF-3.0
+%%BoundingBox: 0 0 444 91
+%%EndComments
+% draws Vienna RNA like colored boxes
+/box { % x1 y1 x2 y2 hue saturation
+  gsave
+  dup 0.3 mul 1 exch sub sethsbcolor
+  exch 3 index sub exch 2 index sub rectfill
+  grestore
+} def
+% draws a box in current color
+/box2 { % x1 y1 x2 y2
+  exch 3 index sub exch 2 index sub rectfill
+} def
+/string { % (Text) x y
+ 6 add
+ moveto
+  show
+} def
+0 91 translate
+1 -1 scale
+/Courier findfont
+[10 0 0 -10 0 0] makefont setfont
+150.0 11.5 156.0 20.0 0.16 1 box
+150.0 20.0 156.0 28.5 0.16 1 box
+150.0 28.5 156.0 37.0 0.16 1 box
+150.0 37.0 156.0 45.5 0.16 1 box
+150.0 45.5 156.0 54.0 0.16 1 box
+228.0 11.5 234.0 20.0 0.16 1 box
+228.0 20.0 234.0 28.5 0.16 1 box
+228.0 28.5 234.0 37.0 0.16 1 box
+228.0 37.0 234.0 45.5 0.16 1 box
+228.0 45.5 234.0 54.0 0.16 1 box
+156.0 11.5 162.0 20.0 0.16 1 box
+156.0 20.0 162.0 28.5 0.16 1 box
+156.0 28.5 162.0 37.0 0.16 1 box
+156.0 37.0 162.0 45.5 0.16 1 box
+156.0 45.5 162.0 54.0 0.16 1 box
+222.0 11.5 228.0 20.0 0.16 1 box
+222.0 20.0 228.0 28.5 0.16 1 box
+222.0 28.5 228.0 37.0 0.16 1 box
+222.0 37.0 228.0 45.5 0.16 1 box
+222.0 45.5 228.0 54.0 0.16 1 box
+162.0 11.5 168.0 20.0 0.16 1 box
+162.0 20.0 168.0 28.5 0.16 1 box
+162.0 28.5 168.0 37.0 0.16 1 box
+162.0 37.0 168.0 45.5 0.16 1 box
+162.0 45.5 168.0 54.0 0.16 1 box
+216.0 11.5 222.0 20.0 0.16 1 box
+216.0 20.0 222.0 28.5 0.16 1 box
+216.0 28.5 222.0 37.0 0.16 1 box
+216.0 37.0 222.0 45.5 0.16 1 box
+216.0 45.5 222.0 54.0 0.16 1 box
+168.0 11.5 174.0 20.0 0.48 1 box
+168.0 20.0 174.0 28.5 0.48 1 box
+168.0 28.5 174.0 37.0 0.48 1 box
+168.0 37.0 174.0 45.5 0.48 1 box
+168.0 45.5 174.0 54.0 0.48 1 box
+210.0 11.5 216.0 20.0 0.48 1 box
+210.0 20.0 216.0 28.5 0.48 1 box
+210.0 28.5 216.0 37.0 0.48 1 box
+210.0 37.0 216.0 45.5 0.48 1 box
+210.0 45.5 216.0 54.0 0.48 1 box
+240.0 11.5 246.0 20.0 0.32 1 box
+240.0 20.0 246.0 28.5 0.32 1 box
+240.0 28.5 246.0 37.0 0.32 1 box
+240.0 37.0 246.0 45.5 0.32 1 box
+240.0 45.5 246.0 54.0 0.32 1 box
+336.0 11.5 342.0 20.0 0.32 1 box
+336.0 20.0 342.0 28.5 0.32 1 box
+336.0 28.5 342.0 37.0 0.32 1 box
+336.0 37.0 342.0 45.5 0.32 1 box
+336.0 45.5 342.0 54.0 0.32 1 box
+246.0 11.5 252.0 20.0 0.32 1 box
+246.0 20.0 252.0 28.5 0.32 1 box
+246.0 28.5 252.0 37.0 0.32 1 box
+246.0 37.0 252.0 45.5 0.32 1 box
+246.0 45.5 252.0 54.0 0.32 1 box
+330.0 11.5 336.0 20.0 0.32 1 box
+330.0 20.0 336.0 28.5 0.32 1 box
+330.0 28.5 336.0 37.0 0.32 1 box
+330.0 37.0 336.0 45.5 0.32 1 box
+330.0 45.5 336.0 54.0 0.32 1 box
+252.0 11.5 258.0 20.0 0.32 1 box
+252.0 20.0 258.0 28.5 0.32 1 box
+252.0 28.5 258.0 37.0 0.32 1 box
+252.0 37.0 258.0 45.5 0.32 1 box
+252.0 45.5 258.0 54.0 0.32 1 box
+324.0 11.5 330.0 20.0 0.32 1 box
+324.0 20.0 330.0 28.5 0.32 1 box
+324.0 28.5 330.0 37.0 0.32 1 box
+324.0 37.0 330.0 45.5 0.32 1 box
+324.0 45.5 330.0 54.0 0.32 1 box
+258.0 11.5 264.0 20.0 0.48 1 box
+258.0 20.0 264.0 28.5 0.48 1 box
+258.0 28.5 264.0 37.0 0.48 1 box
+258.0 37.0 264.0 45.5 0.48 1 box
+258.0 45.5 264.0 54.0 0.48 1 box
+318.0 11.5 324.0 20.0 0.48 1 box
+318.0 20.0 324.0 28.5 0.48 1 box
+318.0 28.5 324.0 37.0 0.48 1 box
+318.0 37.0 324.0 45.5 0.48 1 box
+318.0 45.5 324.0 54.0 0.48 1 box
+264.0 11.5 270.0 20.0 0.32 1 box
+264.0 20.0 270.0 28.5 0.32 1 box
+264.0 28.5 270.0 37.0 0.32 1 box
+264.0 37.0 270.0 45.5 0.32 1 box
+264.0 45.5 270.0 54.0 0.32 1 box
+312.0 11.5 318.0 20.0 0.32 1 box
+312.0 20.0 318.0 28.5 0.32 1 box
+312.0 28.5 318.0 37.0 0.32 1 box
+312.0 37.0 318.0 45.5 0.32 1 box
+312.0 45.5 318.0 54.0 0.32 1 box
+0 setgray
+(.........\(\(\(\(......\)\)\)\).\(\(\(\(\(.......\)\)\)\)\)..........) 96.0 2.0 string
+(SEQ47_2_50_+) 6.0 12.5 string
+(AGGUAU-UAGAAAAAC-CAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC) 96.0 12.5 string
+(49) 408.0 12.5 string
+(SEQ42_1_50_+) 6.0 21.0 string
+(GUAAAUAUAGUUUAAC-CAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC) 96.0 21.0 string
+(50) 408.0 21.0 string
+(SEQ41_1_50_+) 6.0 29.5 string
+(ACUCUUUUAGUAUAAA-UAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC) 96.0 29.5 string
+(50) 408.0 29.5 string
+(SEQ39_1_50_+) 6.0 38.0 string
+(GUUCUUGUAGUUGAAA-UACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU) 96.0 38.0 string
+(50) 408.0 38.0 string
+(SEQ34_1_51_+) 6.0 46.5 string
+(CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU) 96.0 46.5 string
+(51) 408.0 46.5 string
+(.........10........20........30........40........50) 96.0 57.0 string
+0.6 setgray
+96.0 80.9 102.0 85.0 box2
+102.0 80.9 108.0 85.0 box2
+108.0 80.9 114.0 85.0 box2
+114.0 80.9 120.0 85.0 box2
+120.0 80.9 126.0 85.0 box2
+126.0 72.8 132.0 85.0 box2
+132.0 80.9 138.0 85.0 box2
+138.0 68.8 144.0 85.0 box2
+144.0 68.8 150.0 85.0 box2
+150.0 68.8 156.0 85.0 box2
+156.0 72.8 162.0 85.0 box2
+162.0 76.9 168.0 85.0 box2
+168.0 76.9 174.0 85.0 box2
+174.0 68.8 180.0 85.0 box2
+180.0 68.8 186.0 85.0 box2
+186.0 76.9 192.0 85.0 box2
+192.0 84.0 198.0 85.0 box2
+198.0 76.9 204.0 85.0 box2
+204.0 68.8 210.0 85.0 box2
+210.0 80.9 216.0 85.0 box2
+216.0 76.9 222.0 85.0 box2
+222.0 72.8 228.0 85.0 box2
+228.0 72.8 234.0 85.0 box2
+234.0 80.9 240.0 85.0 box2
+240.0 76.9 246.0 85.0 box2
+246.0 76.9 252.0 85.0 box2
+252.0 76.9 258.0 85.0 box2
+258.0 76.9 264.0 85.0 box2
+264.0 80.9 270.0 85.0 box2
+270.0 72.8 276.0 85.0 box2
+276.0 68.8 282.0 85.0 box2
+282.0 76.9 288.0 85.0 box2
+288.0 76.9 294.0 85.0 box2
+294.0 76.9 300.0 85.0 box2
+300.0 72.8 306.0 85.0 box2
+306.0 76.9 312.0 85.0 box2
+312.0 80.9 318.0 85.0 box2
+318.0 80.9 324.0 85.0 box2
+324.0 76.9 330.0 85.0 box2
+330.0 76.9 336.0 85.0 box2
+336.0 76.9 342.0 85.0 box2
+342.0 76.9 348.0 85.0 box2
+348.0 76.9 354.0 85.0 box2
+354.0 76.9 360.0 85.0 box2
+360.0 72.8 366.0 85.0 box2
+366.0 80.9 372.0 85.0 box2
+372.0 76.9 378.0 85.0 box2
+378.0 76.9 384.0 85.0 box2
+384.0 68.8 390.0 85.0 box2
+390.0 76.9 396.0 85.0 box2
+396.0 76.9 402.0 85.0 box2
+showpage
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment1.rnaz.out	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,42 @@
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 5
+ Columns: 51
+ Reading direction: forward
+ Mean pairwise identity:  44.05
+ Shannon entropy: 1.03471
+ G+C content: 0.31965
+ Mean single sequence MFE:  -5.08
+ Consensus MFE:  -7.64
+ Energy contribution:  -3.12
+ Covariance contribution:  -4.52
+ Combinations/Pair:   2.89
+ Mean z-score:   0.22
+ Structure conservation index:   1.50
+ Background model: dinucleotide
+ Decision model: structural RNA alignment quality
+ SVM decision value:   3.53
+ SVM RNA-class probability: 0.999916
+ Prediction: RNA
+
+######################################################################
+
+>SEQ47_2_50_+
+AGGUAU-UAGAAAAAC-CAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC
+.(((..-.......))-)......((((((.....)))))).......... (  -4.20, z-score =   0.02, S)
+>SEQ42_1_50_+
+GUAAAUAUAGUUUAAC-CAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC
+.........((((...-..)))).((((((.....)))))).......... (  -5.90, z-score =  -0.43, R)
+>SEQ41_1_50_+
+ACUCUUUUAGUAUAAA-UAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC
+.........((((...-..)))).(((((.......))))).......... (  -1.80, z-score =   1.22, R)
+>SEQ39_1_50_+
+GUUCUUGUAGUUGAAA-UACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU
+....(((((.......-)))))(((((((.......)))))))........ (  -7.30, z-score =  -0.10, R)
+>SEQ34_1_51_+
+CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU
+..............((((...((((((((.......))))).)))..)))) (  -6.20, z-score =   0.37, R)
+>consensus
+AUGAAUAUAGUUUAAA_UAGAACAUUAGAUUUUCAAACUAAUAGUAGAGGC
+.........((((......)))).(((((.......))))).......... ( -7.64 =  -3.12 +  -4.52) 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment1.sth	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,9 @@
+# STOCKHOLM 1.0
+
+SEQ39_1_50_+          GUUCUUGUAGUUGAAA-UACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU
+SEQ42_1_50_+          GUAAAUAUAGUUUAAC-CAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC
+SEQ47_2_50_+          AGGUAU-UAGAAAAAC-CAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC
+SEQ41_1_50_+          ACUCUUUUAGUAUAAA-UAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC
+SEQ34_1_51_+          CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU
+#=GC SS_cons          .........<<<<......>>>>.<<<<<.......>>>>>..........
+//
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment1_R2R.sto.pdf	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,618 @@
+%PDF-1.0
+5 0 obj
+<<
+/Type /Font
+/Subtype /Type1
+/Name /FH
+/BaseFont /Helvetica
+/Encoding /WinAnsiEncoding
+>>
+endobj
+4 0 obj
+[/PDF /Text /ImageC]
+endobj
+6 0 obj
+<<
+/Type /Page
+/Parent 3 0 R
+/Resources 9 0 R
+/MediaBox [0 0 206.546659 86.571587]
+/Contents 7 0 R
+>>
+endobj
+7 0 obj
+<< /Length 8 0 R>>
+stream
+0 g
+BT
+/FH 12 Tf
+ 0 Tr
+0 77.955587 Td
+(result)Tj
+ET
+8.96 w
+1 J
+1 j
+72 w
+0 J
+0 j
+7.56 w
+1 J
+1 j
+72 w
+0 J
+0 j
+7.56 w
+1 J
+1 j
+72 w
+0 J
+0 j
+1.44 w
+0 G
+92.164227 15.538227 m
+96.052227 15.538227 l
+S
+72 w
+1.44 w
+92.164227 23.098227 m
+96.052227 23.098227 l
+S
+72 w
+.843137 .937255 .772549 rg
+85.070727 33.350727 m
+103.145727 33.350727 l
+103.145727 27.965727 l
+85.070727 27.965727 l
+h
+f
+1.44 w
+92.164227 30.658227 m
+96.052227 30.658227 l
+S
+72 w
+85.070727 40.910727 m
+103.145727 40.910727 l
+103.145727 35.525727 l
+85.070727 35.525727 l
+h
+f
+1.44 w
+92.164227 38.218227 m
+96.052227 38.218227 l
+S
+72 w
+108.002182 18.230727 m
+126.077182 18.230727 l
+126.077182 12.845727 l
+108.002182 12.845727 l
+h
+f
+1.44 w
+115.095682 15.538227 m
+118.983682 15.538227 l
+S
+72 w
+1.44 w
+115.095682 23.098227 m
+118.983682 23.098227 l
+S
+72 w
+108.002182 33.350727 m
+126.077182 33.350727 l
+126.077182 27.965727 l
+108.002182 27.965727 l
+h
+f
+1.44 w
+115.095682 30.658227 m
+118.983682 30.658227 l
+S
+72 w
+1.44 w
+115.095682 38.218227 m
+118.983682 38.218227 l
+S
+72 w
+108.002182 48.470727 m
+126.077182 48.470727 l
+126.077182 43.085727 l
+108.002182 43.085727 l
+h
+f
+1.44 w
+115.095682 45.778227 m
+118.983682 45.778227 l
+S
+72 w
+.5 w
+.360784 G
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+S
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+19.455 7.5 Td
+(R)Tj
+ET
+.72 w
+0 G
+.85098 0 0 rg
+32.28 10.1925 m
+32.28 8.780032 31.134968 7.635 29.7225 7.635 c
+28.310032 7.635 27.165 8.780032 27.165 10.1925 c
+27.165 11.604968 28.310032 12.75 29.7225 12.75 c
+31.134968 12.75 32.28 11.604968 32.28 10.1925 c
+b
+39.84 10.1925 m
+39.84 8.780032 38.694968 7.635 37.2825 7.635 c
+35.870032 7.635 34.725 8.780032 34.725 10.1925 c
+34.725 11.604968 35.870032 12.75 37.2825 12.75 c
+38.694968 12.75 39.84 11.604968 39.84 10.1925 c
+b
+47.4 10.1925 m
+47.4 8.780032 46.254968 7.635 44.8425 7.635 c
+43.430032 7.635 42.285 8.780032 42.285 10.1925 c
+42.285 11.604968 43.430032 12.75 44.8425 12.75 c
+46.254968 12.75 47.4 11.604968 47.4 10.1925 c
+b
+54.96 10.1925 m
+54.96 8.780032 53.814968 7.635 52.4025 7.635 c
+50.990032 7.635 49.845 8.780032 49.845 10.1925 c
+49.845 11.604968 50.990032 12.75 52.4025 12.75 c
+53.814968 12.75 54.96 11.604968 54.96 10.1925 c
+b
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+57.255 7.5 Td
+(U)Tj
+ET
+70.08 10.1925 m
+70.08 8.780032 68.934968 7.635 67.5225 7.635 c
+66.110032 7.635 64.965 8.780032 64.965 10.1925 c
+64.965 11.604968 66.110032 12.75 67.5225 12.75 c
+68.934968 12.75 70.08 11.604968 70.08 10.1925 c
+b
+.85098 0 0 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+72.375 7.5 Td
+(U)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+80.14125 7.5 Td
+(A)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+85.070727 12.845727 Td
+(G)Tj
+ET
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+85.280727 20.405727 Td
+(U)Tj
+ET
+.85098 0 0 rg
+90.545727 30.658227 m
+90.545727 29.245759 89.400696 28.100727 87.988227 28.100727 c
+86.575759 28.100727 85.430727 29.245759 85.430727 30.658227 c
+85.430727 32.070696 86.575759 33.215727 87.988227 33.215727 c
+89.400696 33.215727 90.545727 32.070696 90.545727 30.658227 c
+b
+90.545727 38.218227 m
+90.545727 36.805759 89.400696 35.660727 87.988227 35.660727 c
+86.575759 35.660727 85.430727 36.805759 85.430727 38.218227 c
+85.430727 39.630696 86.575759 40.775727 87.988227 40.775727 c
+89.400696 40.775727 90.545727 39.630696 90.545727 38.218227 c
+b
+BT
+/FH 7.5 Tf
+ 0 Tr
+82.085646 42.27736 Td
+(A)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+84.666009 49.383366 Td
+(A)Tj
+ET
+96.665727 55.071958 m
+96.665727 53.659489 95.520696 52.514458 94.108227 52.514458 c
+92.695759 52.514458 91.550727 53.659489 91.550727 55.071958 c
+91.550727 56.484426 92.695759 57.629458 94.108227 57.629458 c
+95.520696 57.629458 96.665727 56.484426 96.665727 55.071958 c
+b
+BT
+/FH 7.5 Tf
+ 0 Tr
+98.547945 49.383366 Td
+(Y)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+101.128309 42.27736 Td
+(A)Tj
+ET
+102.785727 38.218227 m
+102.785727 36.805759 101.640696 35.660727 100.228227 35.660727 c
+98.815759 35.660727 97.670727 36.805759 97.670727 38.218227 c
+97.670727 39.630696 98.815759 40.775727 100.228227 40.775727 c
+101.640696 40.775727 102.785727 39.630696 102.785727 38.218227 c
+b
+102.785727 30.658227 m
+102.785727 29.245759 101.640696 28.100727 100.228227 28.100727 c
+98.815759 28.100727 97.670727 29.245759 97.670727 30.658227 c
+97.670727 32.070696 98.815759 33.215727 100.228227 33.215727 c
+101.640696 33.215727 102.785727 32.070696 102.785727 30.658227 c
+b
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+97.726977 20.405727 Td
+(A)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+97.520727 12.845727 Td
+(C)Tj
+ET
+.85098 0 0 rg
+108.131455 10.1925 m
+108.131455 8.780032 106.986423 7.635 105.573955 7.635 c
+104.161486 7.635 103.016455 8.780032 103.016455 10.1925 c
+103.016455 11.604968 104.161486 12.75 105.573955 12.75 c
+106.986423 12.75 108.131455 11.604968 108.131455 10.1925 c
+b
+113.477182 15.538227 m
+113.477182 14.125759 112.33215 12.980727 110.919682 12.980727 c
+109.507214 12.980727 108.362182 14.125759 108.362182 15.538227 c
+108.362182 16.950696 109.507214 18.095727 110.919682 18.095727 c
+112.33215 18.095727 113.477182 16.950696 113.477182 15.538227 c
+b
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+108.418432 20.405727 Td
+(Y)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+108.212182 27.965727 Td
+(R)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+108.212182 35.525727 Td
+(R)Tj
+ET
+.85098 0 0 rg
+113.477182 45.778227 m
+113.477182 44.365759 112.33215 43.220727 110.919682 43.220727 c
+109.507214 43.220727 108.362182 44.365759 108.362182 45.778227 c
+108.362182 47.190696 109.507214 48.335727 110.919682 48.335727 c
+112.33215 48.335727 113.477182 47.190696 113.477182 45.778227 c
+b
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+103.324729 48.853431 Td
+(U)Tj
+ET
+.85098 0 0 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+102.921787 56.402685 Td
+(U)Tj
+ET
+112.432518 65.350372 m
+112.432518 63.937904 111.287486 62.792872 109.875018 62.792872 c
+108.46255 62.792872 107.317518 63.937904 107.317518 65.350372 c
+107.317518 66.76284 108.46255 67.907872 109.875018 67.907872 c
+111.287486 67.907872 112.432518 66.76284 112.432518 65.350372 c
+b
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+114.538432 65.070587 Td
+(Y)Tj
+ET
+.85098 0 0 rg
+126.761846 65.350372 m
+126.761846 63.937904 125.616814 62.792872 124.204346 62.792872 c
+122.791877 62.792872 121.646846 63.937904 121.646846 65.350372 c
+121.646846 66.76284 122.791877 67.907872 124.204346 67.907872 c
+125.616814 67.907872 126.761846 66.76284 126.761846 65.350372 c
+b
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+125.948827 56.402685 Td
+(A)Tj
+ET
+.85098 0 0 rg
+130.604635 51.545931 m
+130.604635 50.133462 129.459603 48.988431 128.047135 48.988431 c
+126.634667 48.988431 125.489635 50.133462 125.489635 51.545931 c
+125.489635 52.958399 126.634667 54.103431 128.047135 54.103431 c
+129.459603 54.103431 130.604635 52.958399 130.604635 51.545931 c
+b
+125.717182 45.778227 m
+125.717182 44.365759 124.57215 43.220727 123.159682 43.220727 c
+121.747214 43.220727 120.602182 44.365759 120.602182 45.778227 c
+120.602182 47.190696 121.747214 48.335727 123.159682 48.335727 c
+124.57215 48.335727 125.717182 47.190696 125.717182 45.778227 c
+b
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+120.658432 35.525727 Td
+(Y)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+120.658432 27.965727 Td
+(Y)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+120.452182 20.405727 Td
+(R)Tj
+ET
+.85098 0 0 rg
+125.717182 15.538227 m
+125.717182 14.125759 124.57215 12.980727 123.159682 12.980727 c
+121.747214 12.980727 120.602182 14.125759 120.602182 15.538227 c
+120.602182 16.950696 121.747214 18.095727 123.159682 18.095727 c
+124.57215 18.095727 125.717182 16.950696 125.717182 15.538227 c
+b
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+126.004159 7.5 Td
+(Y)Tj
+ET
+.85098 0 0 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+133.357909 7.5 Td
+(R)Tj
+ET
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+140.917909 7.5 Td
+(R)Tj
+ET
+BT
+/FH 7.5 Tf
+ 0 Tr
+148.477909 7.5 Td
+(U)Tj
+ET
+.85098 0 0 rg
+161.302909 10.1925 m
+161.302909 8.780032 160.157877 7.635 158.745409 7.635 c
+157.332941 7.635 156.187909 8.780032 156.187909 10.1925 c
+156.187909 11.604968 157.332941 12.75 158.745409 12.75 c
+160.157877 12.75 161.302909 11.604968 161.302909 10.1925 c
+b
+168.862909 10.1925 m
+168.862909 8.780032 167.717877 7.635 166.305409 7.635 c
+164.892941 7.635 163.747909 8.780032 163.747909 10.1925 c
+163.747909 11.604968 164.892941 12.75 166.305409 12.75 c
+167.717877 12.75 168.862909 11.604968 168.862909 10.1925 c
+b
+176.422909 10.1925 m
+176.422909 8.780032 175.277877 7.635 173.865409 7.635 c
+172.452941 7.635 171.307909 8.780032 171.307909 10.1925 c
+171.307909 11.604968 172.452941 12.75 173.865409 12.75 c
+175.277877 12.75 176.422909 11.604968 176.422909 10.1925 c
+b
+BT
+/FH 7.5 Tf
+ 0 Tr
+178.507909 7.5 Td
+(G)Tj
+ET
+.501961 .482353 .533333 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+186.277909 7.5 Td
+(R)Tj
+ET
+.85098 0 0 rg
+BT
+/FH 7.5 Tf
+ 0 Tr
+194.044159 7.5 Td
+(Y)Tj
+ET
+1.5 w
+14.6025 10.1925 m
+18.3825 10.1925 l
+S
+0 g
+BT
+/FH 7.5 Tf
+ 0 Tr
+7.5 7.5 Td
+(5´)Tj
+ET
+.5 w
+endstream
+endobj
+10 0 obj<</Type/ExtGState/SA true/OP false/op false/OPM 1/ca 1.0/CA 1.0/BM/Normal/SMask/None/AIS false>>
+endobj
+9 0 obj
+<< /Font <</FH 5 0 R>> /ProcSet[/PDF/Text/ImageC]/XObject << >>/ExtGState<</GS0 10 0 R>>/Properties<</MC0<</Color[20224.0 -32768.0 -1.0]/Title(Layer 1)/Visible true/Preview true/Editable true/Printed true/Dimmed true>>>>>>
+endobj
+8 0 obj
+8854
+endobj
+1 0 obj
+<<
+/Type /Catalog
+/Pages 3 0 R
+/Outlines 2 0 R
+>>
+endobj
+3 0 obj
+<<
+/Type /Pages
+/Count 1
+/Kids [6 0 R ]
+>>
+endobj
+2 0 obj
+<<
+/Type /Outlines
+/Count 0
+>>
+endobj
+xref
+0 11
+0000000000 65535 f 
+0000009544 00000 n 
+0000009667 00000 n 
+0000009609 00000 n 
+0000000116 00000 n 
+0000000009 00000 n 
+0000000152 00000 n 
+0000000269 00000 n 
+0000009524 00000 n 
+0000009286 00000 n 
+0000009174 00000 n 
+trailer
+<<
+/Size 11
+/Root 1 0 R
+>>
+startxref
+9713
+%%EOF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment2.clustal	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,9 @@
+CLUSTAL W --- LocARNA 1.8.10
+
+
+
+SEQ4_526_595_+     CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+SEQ5_526_595_+     CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+SEQ16_526_595_+    CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+SEQ19_523_592_+    CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+SEQ14_529_598_+    CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUUCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment2.cons.tsv	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,2 @@
+	Background model	Columns	Combinations/Pair	Consensus MFE	Covariance contribution	Decision model	Energy contribution	G+C content	Mean pairwise identity	Mean single sequence MFE	Mean z-score	Prediction	Reading direction	SVM RNA-class probability	SVM decision value	Sequences	Shannon entropy	Structure conservation index	alignment	multihit per_species	num_human_seqs_all	num_seqs	num_seqs_all	# seqId	basePairCount	beginPos	bgCykProb	bgProb	cykScore	endPos	fold	posScore	score	strCykProb	strPostProb	strProb	rscape_#target_E-val	rscape_Found	rscape_MSA	rscape_PPV	rscape_SEN	rscape_TP	rscape_True	rscape_alen	rscape_avgid	rscape_method	rscape_nseq	rscape_out	cluster_bed	cluster_human_ids	cluster_human_loc
+0	dinucleotide	70	1.000	-14.410	0.000	structural RNA alignment quality	-14.410	0.497	99.430	-14.750	-0.200	OTHER	forward	0.014	-1.570	5.000	0.010	0.980	cluster.aln	0	0	5	19														0.050		result.aln_1					70	99.430		5	RESULTS/result.aln.sum			
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment2.evofold.out	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,1 @@
+# seqId	beginPos	endPos	basePairCount	strCykProb	bgCykProb	strProb	bgProb	cykScore	score	strPostProb	fold	posScore
Binary file test-data/alignment2.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment2.rnaz.out	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,42 @@
+
+############################  RNAz 2.1  ##############################
+
+ Sequences: 5
+ Columns: 70
+ Reading direction: forward
+ Mean pairwise identity:  99.43
+ Shannon entropy: 0.01031
+ G+C content: 0.49714
+ Mean single sequence MFE: -14.75
+ Consensus MFE: -14.41
+ Energy contribution: -14.41
+ Covariance contribution:   0.00
+ Combinations/Pair:   1.00
+ Mean z-score:  -0.20
+ Structure conservation index:   0.98
+ Background model: dinucleotide
+ Decision model: structural RNA alignment quality
+ SVM decision value:  -1.57
+ SVM RNA-class probability: 0.014380
+ Prediction: OTHER
+
+######################################################################
+
+>SEQ4_526_595_+
+CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+(((((((...((((((((((....))))).......))))))))))))............((....)).. ( -14.41, z-score =  -0.08, R)
+>SEQ5_526_595_+
+CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+(((((((...((((((((((....))))).......))))))))))))............((....)).. ( -14.41, z-score =  -0.08, R)
+>SEQ16_526_595_+
+CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+(((((((...((((((((((....))))).......))))))))))))............((....)).. ( -14.41, z-score =  -0.08, R)
+>SEQ19_523_592_+
+CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+(((((((...((((((((((....))))).......))))))))))))............((....)).. ( -14.41, z-score =  -0.08, R)
+>SEQ14_529_598_+
+CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUUCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+(((((((.((((..((((((....)))))).....))))..)))))))............((....)).. ( -16.10, z-score =  -0.67, R)
+>consensus
+CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+(((((((...((((((((((....))))).......))))))))))))............((....)).. (-14.41 = -14.41 +   0.00) 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment2.sth	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,9 @@
+# STOCKHOLM 1.0
+
+SEQ5_526_595_+           CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+SEQ4_526_595_+           CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+SEQ14_529_598_+          CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUUCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+SEQ19_523_592_+          CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+SEQ16_526_595_+          CUUUGUCCCUGACUGACUAUGCUUGUGGUUCUCCUCCAGUUGAUAGAGAAAAACAACCCAGCGAAGGCGC
+#=GC SS_cons             <<<<<<<...<<<<<<<<<<....>>>>>.......>>>>>>>>>>>>............<<<....>>>
+//
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment2b-transcript.fa	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,73 @@
+>hg38_chr7_27162434_27166719_- Hoxa9-Xtend5UTR
+GTTCCGGAGCTGCGGGGTCTCTTAGGCGAGGCTGCCTTTTCCCAAACCGAACTTGCCTTC
+CATTCATGCCACTTGTAGTTTTTTCCCCAGCTGGGATTCACGGAGCGCAACCAGGCTTGC
+AGCGCTCATGGTTAGAGCCTCTGAGGCTGGAGCACAGGGCTGGGTCGCCAGCCGCCTGCG
+CCTGGGAATCCTGATTGCCAGCTGATGAGAAAGGCGGGCTGGGCGCGCGTGTGCGTGGGG
+TCGAGGGCCGGGGACCGAGCGCGCCGCACAACCAACCAGGCCCTCAAAACCTTCGCCCTG
+GTGGCGGCTGGCCGCTCCCTCCTGGCCAGCTCCTCCGTGGGGTCCTCGTAGCAAAGGCGA
+ATTTAAGGGTTGCCCGGGCGCCCCTCGCTCCAGGCGGGTAGCTGTGGGGACCTACACCCG
+CGGTACTCCCTGAGCGGCCGGTCCCTGCCTGGAGTGCCCTGGTAGGGCCGGCGGCGGCTC
+CGTTTGGGACGGATCCTGCGTTGAATTTGACTTTTCGAGGGCGGCCGCGGGTAAACTCGC
+CTCTCCCGGGGACCGCAGGGATTATTTACAGGGAGCTCGCCAACCAAACACAACAGTCTA
+ACCTTTCCAAGTCCTCGTAAATTTTTACAGCTGGGAGCCACGGCGAGGCAAACGAATCTG
+TTGGTCGTTTCCGACTTCCCGCCAGCCTGTGTGGCTTCTGAAACAATAACTCCTTATGAA
+ATATCATAAATATAGATTTAAATACAGTAGAGCGACAATGCGATTTGGCTGCTTTTTTAT
+GGCTTCAATTATTGTCTAATTTTATGTGAGGGGCTCCGCTGGCCGCACTCGCACGCGGGA
+CCCGCGCCTTCTTGATGGCGTGATTAATTGTGATATAAAATAGTCCGCTTAAGAAGTGTG
+TGTATGGGGGGGGAGACGGGAGAGTACAGAGACAAGGCTAGATTTGATCTTTTAATCGTC
+GTTGGCCACAATTAAAACAAACCCCATCGTAGAGCGGCACGATCCCTTTACATAAAAACA
+TATGGCTTTTGCTATAAAAATTATGACTGCAAAACATCGGACCATTAATAGCGTGCGGAG
+TGATTTACGCGTTATTGTTCTGCTGGACGGGCACGTGACGCGCACGGCCAATGGGGGCGC
+GGGCGCCGGCAACTTATTAGGTGACTGTACTTCCCCCCCGGTGCCACCAAGTTGTTACAT
+GAAATCTGCAGTTTCATAATTTCCGTGGGTCGGGCCGGGCGGGCCAGGCGCTGGGCACGG
+TGATGGCCACCACTGGGGCCCTGGGCAACTACTACGTGGACTCGTTCCTGCTGGGCGCCG
+ACGCCGCGGATGAGCTGAGCGTTGGCCGCTATGCGCCGGGGACCCTGGGCCAGCCTCCCC
+GGCAGGCGGCGACGCTGGCCGAGCACCCCGACTTCAGCCCGTGCAGCTTCCAGTCCAAGG
+CGACGGTGTTTGGCGCCTCGTGGAACCCAGTGCACGCGGCGGGCGCCAACGCTGTACCCG
+CTGCGGTGTaccaccaccatcaccaccacccctacgtgcacccccaggcgcccgtggcgg
+cggcggcgccggacggcAGGTACATGCGCTCCTGGCTGGAGCCCACGCCCGGTGCGCTCT
+CCTTCGCGGGCTTGCCCTCCAGCCGGCCTTATGGCATTAAACCTGAACCGCTGTCGGCCA
+GAAGGGGTGACTGTCCCACGCTTGACACTCACACTTTGTCCCTGACTGACTATGCTTGTG
+GTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGCCTTCTCTGAAAACAATG
+CTGAGAATGAGAGCGGCGGAGACAAGCCCCCCATCGATCCCAGTAAGTGTCTCCTCCCTT
+CAAATCCGCCGCCGCCTCCACGCCGGCCTCCCGGATCTGCTGGCCCGCCAGGTTTCTCTC
+GAGCCTGCCTTCGTCCTCGCTGGAAGCCTCTCGAGTTGGGGCCAGGAGCCAGAAGTTGGT
+GTTTGGGACGCCTCAGATAGGGCCCCAAGTCTGGAGAGCAGTGAAGAGCGGCCCGCAGGG
+CTACGGGAGAGGAGGCGGCTGCTGCAGCGAGAGGGGGCGGGGCGGGCACTTCGGGACGAG
+CCAAGACTGGCCGCCCCTCTCCTTGGCTGCCCAGGCCCAGGACCGAGATACTTTGGGCCG
+TTCTTCGAAAGCAGTGCAGCCCAGAGAGCCTTTTGTACAACTAGATTGTCCGTGAGCGGC
+GGCAGCCAGGGCAGCCGGAGCTGGGACGCTGGGGGAGACGGCCGATTCCTTCCACTTCTT
+GCCTTCGGCCAGTGGCGGCGTAAATCCTGCCAAGATGAGGCTGCGGGCGACCCGGGCCAC
+AAGGGTCCCCATGACAGATTATTCAAATAAGCCACAGACGTGATCAGCGGCCTTAGGGCG
+CCCTGACGGCTTGCCCAGCTCCGAAGGCCTTCCAGGAAGGTTAAATAAGGAGTGGGGGGC
+GTAGAGGGACAGGTTGGGAAAGAAAGACGAAGTCAGTGAACGGGACAGAGGAATCCTAAT
+CTTGCTACAGAACACAAGGCAGCATGCTTTCCCTCTGCGTGGCAAGGAGACCTGTTTCCA
+AATTTCATTCTATACAGCGTTTTGAGAGTGGGAGGAAGGAGAAGGGGGACAAGAGGACAG
+AGTAGGAGAAAGGAAGGTCTCGGAGGGGAGGGCGAGCCAAAGTTTTACTGCGTGCAATTT
+TAAGTGACTGTCTGTGCGTCTGTCTGCCAGGGTTCCATTGTGTCCGAGGCCTGACTGCCT
+TTCCTAACCAGTTCAGCAGAGTTCTGCACTTCGGCCAGAGACCCCATGCAGGAGGCTCAT
+TTGCCCCAGCGGGATGTGCGTCTTCTGCTCCTAAACCCAGTGTTTCTCTTCCCCGCAGAT
+AACCCAGCAGCCAACTGGCTTCATGCGCGCTCCACTCGGAAAAAGCGGTGCCCCTATACA
+AAACACCAGACCCTGGAACTGGAGAAAGAGTTTCTGTTCAACATGTACCTCACCAGGGAC
+CGCAGGTACGAGGTGGCTCGACTGCTCAACCTCACCGAGAGGCAGGTCAAGATCTGGTTC
+CAGAACCGCAGGATGAAAATGAAGAAAATCAACAAAGACCGAGCAAAAGACGAGTGATGC
+CATTTGGGCTTATTTAGAAAAAAGGGTAAGCTAGAGAGAAAAAGAAAGAACTGTCCGTCC
+CCCTTCCGCCTTCTCCCTTCTCTCACCCCCACCCTAGCCTCCACCATCCCCGCACAAAGC
+GGCTCTAAACCTCAGGCCACATCTTTTCCAAGGCAAACCCTGTTCAGGCTGGCTCGTAGG
+CCTGCCGCTTTGATGGAGGAGGTATTGTAAGCTTTCCATTTTCTATAAGAAAAAGGAAAA
+GTTGAGGGGGGGGCATTAGTGCTGATAGCTGTGTGTGTTAGCTTGTATATATATTTTTAA
+AAATCTACCTGTTCCTGACTTAAAACAAAAGGAAAGAAACTACCTTTTTATAATGCACAA
+CTGTTGATGGTAGGCTGTATAGTTTTTAGTCTGTGTAGTTAATTTAATTTGCAGTTTGTG
+CGGCAGATTGCTCTGCCAAGATACTTGAACACTGTGTTTTATTGTGGTAATTATGTTTTG
+TGATTCAAACTTCTGTGTACTGGGTGATGCACCCATTGTGATTGTGGAAGATAGAATTCA
+ATTTGAACTCAGGTTGTTTATGAGGGGAAAAAAACAGTTGCATAGAGTATAGCTCTGTAG
+TGGAATATGTCTTCTGTATAACTAGGCTGTTAACCTATGATTGTAAAGTAGCTGTAAGAA
+TTTCCCAGTGAAATAAAAAAAAATTTTAAGTGTTCTCGGGGATGCATAGATTCATCATTT
+TCTCCACCTTAAAAATGCGGGCATTTAAGTCTGTCCATTATCTATATAGTCCTGTCTTGT
+CTATTGTATATATAATCTATATGATTAAAGAAAATATGCATAATCAGACAAGCTTGAATA
+TTGTTTTTGCACCAGACGAACAGTGAGGAAATTCGGAGCTATACATATGTGCAGAAGGTT
+ACTACCTAGGGTTTATGCTTAATTTTAATTGGAGGAAATGAATGCTGATTGTAACGGAGT
+TAATTTTATTGATAATAAATTATACACTATGAAACCGCCATTGGGCTACTGTAGATTTGT
+ATCCTTGATGAATCTGGGGTTTCCATCAGACTGAACTTACACTGTATATTTTGCAATAGT
+TACCTCAAGGCCTACTGACCAAATTGTTGTGTTGAGATGATATTTAACTTTTTGCCAAAT
+AAAATATATTGATTCTTTTCTATTTT
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignment2b.cons.tsv	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,2 @@
+	Background model	Columns	Combinations/Pair	Consensus MFE	Covariance contribution	Decision model	Energy contribution	G+C content	Mean pairwise identity	Mean single sequence MFE	Mean z-score	Prediction	Reading direction	SVM RNA-class probability	SVM decision value	Sequences	Shannon entropy	Structure conservation index	alignment	multihit per_species	num_human_seqs_all	num_seqs	num_seqs_all	# seqId	basePairCount	beginPos	bgCykProb	bgProb	cykScore	endPos	fold	posScore	score	strCykProb	strPostProb	strProb	rscape_#target_E-val	rscape_Found	rscape_MSA	rscape_PPV	rscape_SEN	rscape_TP	rscape_True	rscape_alen	rscape_avgid	rscape_method	rscape_nseq	rscape_out	cluster_bed	cluster_human_ids	cluster_human_loc
+0	dinucleotide	70	1.000	-14.410	0.000	structural RNA alignment quality	-14.410	0.497	99.430	-14.750	-0.200	OTHER	forward	0.014	-1.570	5.000	0.010	0.980	cluster.aln	0	1	5	19														0.050		result.aln_1					70	99.430		5	RESULTS/result.aln.sum			
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster1.all	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,12 @@
+SEQ44#1#51#+  RESULT  2  CM_SCORE  43.7  MODEL     1.3  ORIGID  RF00005_rep.46_AF347015.1/1604-1672_44      ORIGHEAD  RF00005_rep.46  
+SEQ8#1#48#+   RESULT  2  CM_SCORE  39.1  MODEL     1.3  ORIGID  RF00005_rep.13_AC067849.6/4771-4840_8       ORIGHEAD  RF00005_rep.13  
+SEQ47#2#50#+  RESULT  2  CM_SCORE  38.0  MODEL     1.3  ORIGID  RF00005_rep.6_X93334.1/6942-7009_47         ORIGHEAD  RF00005_rep.6   
+SEQ48#1#52#+  RESULT  2  CM_SCORE  37.9  MODEL     1.3  ORIGID  RF00005_rep.7_AF347005.1/12268-12338_48     ORIGHEAD  RF00005_rep.7   
+SEQ43#1#52#+  RESULT  2  CM_SCORE  35.3  MODEL     1.3  ORIGID  RF00005_rep.45_AF382005.1/581-651_43        ORIGHEAD  RF00005_rep.45  
+SEQ39#1#50#+  RESULT  2  CM_SCORE  28.6  MODEL     1.3  ORIGID  RF00005_rep.41_AC093311.2/140036-139968_39  ORIGHEAD  RF00005_rep.41  
+SEQ34#1#51#+  RESULT  2  CM_SCORE  22.2  MODEL     1.3  ORIGID  RF00005_rep.37_AF347001.1/16015-15948_34    ORIGHEAD  RF00005_rep.37  
+SEQ42#1#50#+  RESULT  2  CM_SCORE  45.6  CMSEARCH  1.3  ORIGID  RF00005_rep.44_AC008670.6/83597-83665_42    ORIGHEAD  RF00005_rep.44  
+SEQ38#1#50#+  RESULT  2  CM_SCORE  45.2  CMSEARCH  1.3  ORIGID  RF00005_rep.40_AF382013.1/10403-10467_38    ORIGHEAD  RF00005_rep.40  
+SEQ6#1#51#+   RESULT  2  CM_SCORE  43.6  CMSEARCH  1.3  ORIGID  RF00005_rep.11_AF346992.1/15890-15955_6     ORIGHEAD  RF00005_rep.11  
+SEQ41#1#50#+  RESULT  2  CM_SCORE  40.6  CMSEARCH  1.3  ORIGID  RF00005_rep.43_L23320.1/77-10_41            ORIGHEAD  RF00005_rep.43  
+SEQ49#1#50#+  RESULT  2  CM_SCORE  35.7  CMSEARCH  1.3  ORIGID  RF00005_rep.8_AF134583.1/1599-1666_49       ORIGHEAD  RF00005_rep.8   
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster1.all.fa	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,24 @@
+>SEQ34_1_51_+ RESULT 2 SCORE 22.2 EVALUE 1.9e-06 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005_rep.37
+CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUU
+>SEQ41_1_50_+ RESULT 2 SCORE 40.6 EVALUE 3.3e-14 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005_rep.43
+ACUCUUUUAGUAUAAAUAGUACCGUUAACUUCCAAUUAACUAGUUUUGAC
+>SEQ47_2_50_+ RESULT 2 SCORE 38.0 EVALUE 4e-13 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6
+AGGUAUUAGAAAAACCAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGC
+>SEQ42_1_50_+ RESULT 2 SCORE 45.6 EVALUE 2.6e-16 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44
+GUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGC
+>SEQ39_1_50_+ RESULT 2 SCORE 28.6 EVALUE 3.7e-09 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41
+GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGU
+>SEQ43_1_52_+ RESULT 2 SCORE 35.3 EVALUE 5.8e-12 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45
+GUUUAUGUAGCUUACCUCCUCAAAGCAAUACACUGAAAAUGUUUAGACGGGC
+>SEQ49_1_50_+ RESULT 2 SCORE 35.7 EVALUE 3.9e-12 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005_rep.8
+AGAAAUUUAGGUUAAAUACAGACCAAGAGCCUUCAAAGCCCUCAGUAAGU
+>SEQ44_1_51_+ RESULT 2 SCORE 43.7 EVALUE 1.7e-15 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005_rep.46
+CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAAC
+>SEQ8_1_48_+ RESULT 2 SCORE 39.1 EVALUE 1.4e-13 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13
+CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAG
+>SEQ6_1_51_+ RESULT 2 SCORE 43.6 EVALUE 1.7e-15 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11
+GUCCUUGUAGUAUAAACUAAUACACCAGUCUUGUAAACCGGAGAUGAAAAC
+>SEQ38_1_50_+ RESULT 2 SCORE 45.2 EVALUE 3.9e-16 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40
+UGGUAUAUAGUUUAAACAAAACGAAUGAUUUCGACUCAUUAAAUUAUGAU
+>SEQ48_1_52_+ RESULT 2 SCORE 37.9 EVALUE 4.5e-13 CLUSTER 1.3 LOC MISS ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005_rep.7
+ACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGCCCCAAAAAUUUUGGU
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster2.all	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,19 @@
+SEQ4#526#595#+   RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  gorGor3_4   ORIGHEAD  gorGor3  
+SEQ5#526#595#+   RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  ponAbe2_5   ORIGHEAD  ponAbe2  
+SEQ1#526#595#+   RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  hg38_1      ORIGHEAD  hg38     
+SEQ3#526#595#+   RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  panPan1_3   ORIGHEAD  panPan1  
+SEQ8#526#595#+   RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  macFas5_8   ORIGHEAD  macFas5  
+SEQ10#526#595#+  RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  chlSab2_10  ORIGHEAD  chlSab2  
+SEQ11#526#595#+  RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  nasLar1_11  ORIGHEAD  nasLar1  
+SEQ2#526#595#+   RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  panTro4_2   ORIGHEAD  panTro4  
+SEQ12#526#595#+  RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  rhiRox1_12  ORIGHEAD  rhiRox1  
+SEQ7#526#595#+   RESULT  1  CM_SCORE  136.4  MODEL     1.1  ORIGID  rheMac3_7   ORIGHEAD  rheMac3  
+SEQ14#529#598#+  RESULT  1  CM_SCORE  129.7  MODEL     1.1  ORIGID  saiBol1_14  ORIGHEAD  saiBol1  
+SEQ18#527#596#+  RESULT  1  CM_SCORE  129.7  MODEL     1.1  ORIGID  tupBel1_18  ORIGHEAD  tupBel1  
+SEQ15#529#598#+  RESULT  1  CM_SCORE  128.6  MODEL     1.1  ORIGID  tarSyr2_15  ORIGHEAD  tarSyr2  
+SEQ16#526#595#+  RESULT  1  CM_SCORE  136.4  CMSEARCH  1.1  ORIGID  micMur1_16  ORIGHEAD  micMur1  
+SEQ19#523#592#+  RESULT  1  CM_SCORE  136.4  CMSEARCH  1.1  ORIGID  mm10_19     ORIGHEAD  mm10     
+SEQ17#526#595#+  RESULT  1  CM_SCORE  136.4  CMSEARCH  1.1  ORIGID  otoGar3_17  ORIGHEAD  otoGar3  
+SEQ9#444#513#+   RESULT  1  CM_SCORE  136.4  CMSEARCH  1.1  ORIGID  papAnu2_9   ORIGHEAD  papAnu2  
+SEQ6#526#595#+   RESULT  1  CM_SCORE  132.7  CMSEARCH  1.1  ORIGID  nomLeu3_6   ORIGHEAD  nomLeu3  
+SEQ20#525#594#+  RESULT  1  CM_SCORE  129.1  CMSEARCH  1.1  ORIGID  canFam3_20  ORIGHEAD  canFam3  
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cluster2.all.fa	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,38 @@
+>SEQ4_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID gorGor3_4 ORIGHEAD gorGor3
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ5_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID ponAbe2_5 ORIGHEAD ponAbe2
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ16_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID micMur1_16 ORIGHEAD micMur1
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ19_523_592_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID mm10_19 ORIGHEAD mm10
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ14_529_598_+ RESULT 1 SCORE 129.7 EVALUE 3.3e-33 CLUSTER 1.1 LOC MISS ORIGID saiBol1_14 ORIGHEAD saiBol1
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTTCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ17_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID otoGar3_17 ORIGHEAD otoGar3
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ1_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID hg38_1 ORIGHEAD hg38
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ3_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID panPan1_3 ORIGHEAD panPan1
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ8_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID macFas5_8 ORIGHEAD macFas5
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ10_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID chlSab2_10 ORIGHEAD chlSab2
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ11_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID nasLar1_11 ORIGHEAD nasLar1
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ20_525_594_+ RESULT 1 SCORE 129.1 EVALUE 4.5e-33 CLUSTER 1.1 LOC MISS ORIGID canFam3_20 ORIGHEAD canFam3
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAGCCCAGCGAAGGCGC
+>SEQ15_529_598_+ RESULT 1 SCORE 128.6 EVALUE 6.3e-33 CLUSTER 1.1 LOC MISS ORIGID tarSyr2_15 ORIGHEAD tarSyr2
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACCACCCAGCGAAGGCGC
+>SEQ2_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID panTro4_2 ORIGHEAD panTro4
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ18_527_596_+ RESULT 1 SCORE 129.7 EVALUE 3.3e-33 CLUSTER 1.1 LOC MISS ORIGID tupBel1_18 ORIGHEAD tupBel1
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAGCAATCCAGCGAAGGCGC
+>SEQ12_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID rhiRox1_12 ORIGHEAD rhiRox1
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ9_444_513_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID papAnu2_9 ORIGHEAD papAnu2
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ7_526_595_+ RESULT 1 SCORE 136.4 EVALUE 7.9e-35 CLUSTER 1.1 LOC MISS ORIGID rheMac3_7 ORIGHEAD rheMac3
+CTTTGTCCCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
+>SEQ6_526_595_+ RESULT 1 SCORE 132.7 EVALUE 6.4e-34 CLUSTER 1.1 LOC MISS ORIGID nomLeu3_6 ORIGHEAD nomLeu3
+CTTTGTCTCTGACTGACTATGCTTGTGGTTCTCCTCCAGTTGATAGAGAAAAACAACCCAGCGAAGGCGC
Binary file test-data/structure1.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/structure1.ps	Sat Oct 27 13:21:39 2018 -0400
@@ -0,0 +1,352 @@
+%!PS-Adobe-3.0 EPSF-3.0
+%%Creator: ViennaRNA-2.2.10
+%%CreationDate: Sat Oct 27 14:38:56 2018
+%%Title: RNA Secondary Structure Plot
+%%BoundingBox: 66 210 518 662
+%%DocumentFonts: Helvetica
+%%Pages: 1
+%%EndComments
+
+%Options: --noLP 
+% to switch off outline pairs of sequence comment or
+% delete the appropriate line near the end of the file
+
+%%BeginProlog
+/RNAplot 100 dict def
+RNAplot begin
+/fsize  14 def
+/outlinecolor {0.2 setgray} bind def
+/paircolor    {0.2 setgray} bind def
+/seqcolor     {0   setgray} bind def
+/cshow  { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def
+/min { 2 copy gt { exch } if pop } bind def
+/max { 2 copy lt { exch } if pop } bind def
+/arccoords { % i j arccoords
+  % 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
+RNAplot begin
+% extra definitions for standard anotations
+/min { 2 copy gt { exch } if pop } bind def
+/BLACK { 0 0 0 } def
+/RED   { 1 0 0 } def
+/GREEN { 0 1 0 } def
+/BLUE  { 0 0 1 } def
+/WHITE { 1 1 1 } def
+/LabelFont { % font size LabelFont
+  exch findfont exch fsize mul scalefont setfont
+} bind def
+/Label { % i dx dy (text) Label
+  % write text at base i plus offset dx, dy
+  4 3 roll 1 sub coor exch get aload pop moveto
+  3 1 roll fsize mul exch fsize mul exch rmoveto
+  show
+} bind def
+/cmark { % i cmark   draw circle around base i
+  newpath 1 sub coor exch get aload pop
+  fsize 2 div 0 360 arc stroke
+} bind def
+/gmark { % i j c gmark
+  % draw basepair i,j with c counter examples in gray
+  gsave
+  3 min [0 0.33 0.66 0.9] exch get setgray
+  1 sub dup coor exch get aload pop moveto
+  sequence exch 1 getinterval cshow
+  1 sub dup coor exch get aload pop moveto
+  sequence exch 1 getinterval cshow
+  grestore
+} bind def
+/segmark { % f i j lw r g b segmark
+  % mark segment [i,j] with outline width lw and color rgb
+  % use omark and Fomark instead
+  gsave
+  setrgbcolor setlinewidth
+  newpath
+  1 sub exch 1 sub dup
+  coor exch get aload pop moveto
+  currentdict (cpr) known
+  {
+    3 -1 roll dup 4 1 roll dup
+    {
+      3 1 roll dup 3 -1 roll dup
+      4 1 roll exch 5 2 roll exch
+    }
+    {
+      3 1 roll exch
+    } ifelse
+    1 exch { coor exch get aload pop lineto } for
+    {
+      dup 3 1 roll 1 add exch 1 add arccoords pop pop
+      4 2 roll 5 -1 roll coor exch get aload pop curveto
+    } if
+  }
+  {
+    exch 1 exch {
+      coor exch get aload pop lineto
+    } for
+  } ifelse
+  { closepath fill } if  stroke
+  grestore
+} bind def
+/omark { % i j lw r g b omark
+  % stroke segment [i..j] with linewidth lw, color rgb
+  false 7 1 roll segmark
+} bind def
+/Fomark { % i j r g b Fomark
+  % fill segment [i..j] with color rgb
+  % should precede drawbases
+  1 4 1 roll true 7 1 roll segmark
+} bind def
+/BFmark{ % i j k l r g b BFmark
+  % fill block between pairs (i,j) and (k,l) with color rgb
+  % should precede drawbases
+  gsave
+  setrgbcolor
+  newpath
+  currentdict (cpr) known
+  {
+    dup 1 sub coor exch get aload pop moveto % move to l
+    dup 1 sub 4 -1 roll dup 5 1 roll 1 sub 1 exch
+    { coor exch get aload pop lineto } for % lines from l to j
+    3 -1 roll 4 -1 roll dup 5 1 roll arccoords curveto % curve from j to i
+    exch dup 4 -1 roll 1 sub exch 1 sub 1 exch
+    { coor exch get aload pop lineto } for % lines from i to k
+    exch arccoords curveto% curve from k to l
+  }
+  {  exch 4 3 roll exch 1 sub exch 1 sub dup
+     coor exch get aload pop moveto
+     exch 1 exch { coor exch get aload pop lineto } for
+     exch 1 sub exch 1 sub dup
+     coor exch get aload pop lineto
+     exch 1 exch { coor exch get aload pop lineto } for
+  } ifelse
+    closepath fill stroke
+   grestore
+} bind def
+/hsb {
+  dup 0.3 mul 1 exch sub sethsbcolor
+} bind def
+/colorpair { % i j hue sat colorpair
+  % draw basepair i,j in color
+  % 1 index 0.00 ne {
+  gsave
+  newpath
+  hsb
+  fsize setlinewidth
+  currentdict (cpr) known
+  {
+    exch dup
+    coor  exch 1 sub get aload pop moveto
+    exch arccoords curveto
+  }
+  { 1 sub coor exch get aload pop moveto
+    1 sub coor exch get aload pop lineto
+  } ifelse
+   stroke
+   grestore
+   % } if
+} bind def
+end
+
+%%EndProlog
+RNAplot begin
+% data start here
+/sequence (\
+AUGAAUAUAGUUUAAA_UAGAACAUUAGAUUUUCAAACUAAUAGUAGAGGC\
+) def
+/coor [
+[95.00124359 138.88397217]
+[87.89935303 137.28974915]
+[81.21456146 134.41014099]
+[75.17730713 130.34443665]
+[69.99568176 125.23274994]
+[65.84830475 119.25129700]
+[62.87813568 112.60626221]
+[61.18754959 105.52667999]
+[60.83482361 98.25659943]
+[61.83211517 91.04661560]
+[48.15361786 84.89042664]
+[34.47511673 78.73423004]
+[20.79662132 72.57804108]
+[6.11008787 78.41596222]
+[-8.36961174 72.08241272]
+[-14.05193043 57.33497620]
+[-7.56564760 42.92304993]
+[7.24103928 37.39696503]
+[21.58358574 44.03525925]
+[26.95281219 58.89954376]
+[40.63130951 65.05573273]
+[54.30980682 71.21192932]
+[67.98830414 77.36811829]
+[94.10119629 61.24235916]
+[123.82917786 68.86929321]
+[135.05683899 58.92245483]
+[146.28450012 48.97561264]
+[157.51216125 39.02877426]
+[168.73982239 29.08193398]
+[168.13914490 13.45589161]
+[177.76402283 1.13129318]
+[193.06988525 -2.07256317]
+[206.82977295 5.35708570]
+[212.54667664 19.91218758]
+[207.52125549 34.72026825]
+[194.12637329 42.78940201]
+[178.68666077 40.30959702]
+[167.45899963 50.25643539]
+[156.23133850 60.20327377]
+[145.00367737 70.15011597]
+[133.77601624 80.09695435]
+[136.87315369 86.68378448]
+[138.69926453 93.72961426]
+[139.19142151 100.99159241]
+[138.33265686 108.21938324]
+[136.15257263 115.16385651]
+[132.72630310 121.58563232]
+[128.17196655 127.26335907]
+[122.64655304 132.00131226]
+[116.34051514 135.63619995]
+[109.47121429 138.04269409]
+] def
+/pairs [
+[10 23]
+[11 22]
+[12 21]
+[13 20]
+[25 41]
+[26 40]
+[27 39]
+[28 38]
+[29 37]
+] def
+
+init
+
+% Start Annotations
+10 23 0.16 1 colorpair
+11 22 0.16 1 colorpair
+12 21 0.16 1 colorpair
+13 20 0.48 1 colorpair
+25 41 0.32 1 colorpair
+26 40 0.32 1 colorpair
+27 39 0.32 1 colorpair
+28 38 0.48 1 colorpair
+29 37 0.32 1 colorpair
+
+% End Annotations
+% switch off outline pairs or bases by removing these lines
+drawoutline
+drawpairs
+drawbases
+% Start Annotations
+23 cmark
+11 cmark
+22 cmark
+12 cmark
+21 cmark
+13 cmark
+20 cmark
+25 cmark
+41 cmark
+26 cmark
+40 cmark
+27 cmark
+39 cmark
+28 cmark
+38 cmark
+29 cmark
+37 cmark
+
+% End Annotations
+% show it
+showpage
+end
+%%EOF
Binary file test-data/structure2.png has changed