# HG changeset patch
# User yhoogstrate
# Date 1456760617 18000
# Node ID 59ab674be4b5bda6753442204ba25f0cd679805b
# Parent  eccb5ee89df7a29426659fded521515a68c1f473
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty

diff -r eccb5ee89df7 -r 59ab674be4b5 energy-estimation-utility.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/energy-estimation-utility.xml	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,110 @@
+<tool id="energy_estimation_utility" name="energy-estimation-utility" version="1.6.0_0">
+    <description>Estimate the maximal energy a segment needs to assign to become part of the optimal structure using segmentation-fold</description>
+    
+    <requirements>
+        <requirement type="package" version="1.6.0">segmentation-fold</requirement>
+    </requirements>
+    
+    <stdio></stdio>
+    
+    <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
+    
+    <command><![CDATA[
+        energy-estimation-utility
+            #if $parameters.use_custom_xml == "true"
+                -x "${parameters.input_xml}"
+            #else
+                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
+            #end if
+            
+            -r ${randomization.shuffle_n_times}
+        > "${output_list}"
+    ]]></command>
+    
+    <inputs>
+        <conditional name="parameters">
+            <param name="use_custom_xml"
+                type="boolean"
+                truevalue="true"
+                falsevalue="false"
+                selected="false"
+                label="Use segment definition from history" />
+
+            <when value="false" />
+            <when value="true">
+                <param name="input_xml"
+                    type="data"
+                    format="xml"
+                    multiple="false"
+                    argument="-x"
+                    label="Custom 'segments.xml'-syntaxed file" />
+            </when>
+        </conditional>
+        
+        <conditional name="randomization">
+            <param name="do_randomization"
+                type="boolean"
+                truevalue="true"
+                falsevalue="false"
+                selected="false"
+                label="Randomly shuffle the sequence(s) instead"
+                help="This can be helpful in determining a baseline of observing an energy parameter by chance" />
+
+            <when value="false">
+                <param name="shuffle_n_times"
+                       type="hidden"
+                       value="0"/>
+            </when>
+            <when value="true">
+                <param name="shuffle_n_times"
+                       type="integer"
+                       min="0"
+                       value="10" 
+                       argument="-r"
+                       label="Number of times the sequences have to be shuffled and energy parameters have to be estimated on" />
+            </when>
+        </conditional>
+    </inputs>
+    
+    <outputs>
+        <data format="text" name="output_list" label="${tool.name}" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param  name="use_custom_xml" value="true" />
+            <param  name="input_xml" value="segments_truncated.xml" ftype="xml" />
+            <param  name="do_randomization" value="false" />
+            <param  name="shuffle_n_times" value="0" />
+            
+            <output name="output_list" file="segments_truncated.out.txt" />
+        </test>
+        <test>
+            <param  name="use_custom_xml" value="true" />
+            <param  name="input_xml" value="segments_truncated.xml" ftype="xml" />
+            <param  name="do_randomization" value="false" />
+            <param  name="shuffle_n_times" value="1" />
+            
+            <output name="output_list" file="segments_truncated.out.txt" lines_diff="8" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+The tool uses the sequences from the xml file.
+    ]]></help>
+    
+    <citations>
+        <citation type="bibtex">
+           @mastersthesis{mastersthesis,
+              author       = {Youri Hoogstrate}, 
+              title        = {An algorithm for predicting RNA 2D structures including K-turns},
+              school       = {University of Technology Delft, Leiden University},
+              year         = 2012,
+              address      = {},
+              month        = 11,
+              note         = {Research assignment for Master Computer-science},
+              url          = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
+            }
+        </citation>
+    </citations>
+</tool>
diff -r eccb5ee89df7 -r 59ab674be4b5 scan-for-segments.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scan-for-segments.xml	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,103 @@
+<tool id="scan_for_segments" name="scan-for-segments" version="1.6.0_0">
+    <description>Scan for the presence of segments in sequences using segmentation-fold</description>
+    
+    <requirements>
+        <requirement type="package" version="1.6.0">segmentation-fold</requirement>
+    </requirements>
+    
+    <stdio></stdio>
+    
+    <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
+    
+    <command><![CDATA[
+        scan-for-segments
+            -T \${GALAXY_SLOTS:-4}
+            #if $parameters.use_custom_xml == "true"
+                -x "${parameters.input_xml}"
+            #else
+                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
+            #end if
+            -p "in-depth"
+            "${input_fasta}"
+            
+            >   $output_list
+    ]]></command>
+
+    <inputs>
+        <param name="input_fasta"
+               type="data"
+               format="fasta"
+               argument="-f"
+               label="Fasta file with RNA-sequece" />
+
+        <conditional name="parameters">
+            <param name="use_custom_xml"
+                type="boolean"
+                truevalue="true"
+                falsevalue="false"
+                selected="false"
+                label="Use segment definition from history" />
+
+            <when value="false" />
+            <when value="true">
+                <param name="input_xml"
+                    type="data"
+                    format="xml"
+                    multiple="false"
+                    argument="-x"
+                    label="Custom 'segments.xml'-syntaxed file" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="text" name="output_list" label="${tool.name} on ${str($input_fasta.hid) + ': ' + $input_fasta.name}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_fasta" value="SNORD13-revised.fa" ftype="fasta" />
+            <param name="use_custom_xml" value="false" ftype="fasta" />
+            
+            <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
+        </test>
+        <test>
+            <param name="input_fasta" value="SNORD48-revised.fa" ftype="fasta" />
+            <param name="use_custom_xml" value="false" ftype="fasta" />
+            
+            <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
+        </test>
+        <test>
+            <param name="input_fasta" value="SNORD114-4-revised.fa" ftype="fasta" />
+            <param name="use_custom_xml" value="false" ftype="fasta" />
+            
+            <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
+        </test>
+        <test>
+            <param name="input_fasta" value="SNORD118-revised.fa" ftype="fasta" />
+            <param name="use_custom_xml" value="false" ftype="fasta" />
+            
+            <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
+If present, it will also scan for the Gibbs free energy necessairy the segment has to provide to contribute to the optimal structure.
+    ]]></help>
+    
+    <citations>
+        <citation type="bibtex">
+           @mastersthesis{mastersthesis,
+              author       = {Youri Hoogstrate}, 
+              title        = {An algorithm for predicting RNA 2D structures including K-turns},
+              school       = {University of Technology Delft, Leiden University},
+              year         = 2012,
+              address      = {},
+              month        = 11,
+              note         = {Research assignment for Master Computer-science},
+              url          = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
+            }
+        </citation>
+    </citations>
+</tool>
diff -r eccb5ee89df7 -r 59ab674be4b5 segmentation-fold.xml
--- a/segmentation-fold.xml	Wed Dec 02 04:34:50 2015 -0500
+++ b/segmentation-fold.xml	Mon Feb 29 10:43:37 2016 -0500
@@ -1,8 +1,8 @@
-<tool id="segmentation_fold" name="segmentation-fold" version="1.1.0_1">
+<tool id="segmentation_fold" name="segmentation-fold" version="1.6.0_0">
     <description>RNA-Folding including predefined segments including K-turns</description>
     
     <requirements>
-        <requirement type="package" version="1.1.0">segmentation-fold</requirement>
+        <requirement type="package" version="1.6.0">segmentation-fold</requirement>
     </requirements>
     
     <stdio></stdio>
@@ -15,16 +15,16 @@
             #if $input.method == "fasta"
                 -f $input.input_fasta
             #else
-                -s ${input.input_sequence}
+                -s $input.input_sequence
             #end if
             
             -p $predict_segments
             -h $min_hairpin_size
             
             #if $parameters.settings == "default"
-                -x "${SEGMENTATION_FOLD_DEFAULT_XML}"
+                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
             #else
-                -x $parameters.input_xml
+                -x "${parameters.input_xml}"
             #end if
             
             -t \${GALAXY_SLOTS:-4}
@@ -32,7 +32,6 @@
     ]]></command>
     
     <inputs>
-        
         <conditional name="input">
             <param name="method" type="select" label="Energy parameters">
                 <option value="fasta" selected="true">As FASTA-file</option>
@@ -62,7 +61,8 @@
     </inputs>
     
     <outputs>
-        <data format="dot-bracket" name="output_dbn" label="${tool.name} on ${input.input_fasta.hid + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />
+        <data format="dot-bracket" name="output_dbn" label="asdasdasd" />
+        <!--<data format="dot-bracket" name="output_dbn" label="${tool.name} on ${str(input.input_fasta.hid) + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />-->
     </outputs>
     
     <tests>
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/SNORD114-4-revised.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD114-4-revised.fa	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,2 @@
+>SNORD114-4 revised
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/SNORD114-4-revised.scan-for-segments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD114-4-revised.scan-for-segments.txt	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,124 @@
+>SNORD114-4 x Kt-CD-box.AGA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UAA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-42.dra
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CUG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.AGG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-42.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Loop-E-Motif.bac
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.ACG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.ACA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-G2nA-SAMribo.bsu
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UGU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UGG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-42.tth
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UCA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UCG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-7 G2nA SAM riboswitch (H. marismortui)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UAG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GAA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CGG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-15.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+.(((((((((.......))))))(.(.((((..((..((((((..........)))))).))..)))).).))))	.((((((.((.(((.((.....((((((.(....)....))))))..)...)))).......)).....))))))	-8.12001228333
+>SNORD114-4 x Kt-CD-box.CAG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-U4b.hsa
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-7 (E. coli)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-7 (D. radiodurans)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-58.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UUG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-46.tth
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.AUG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UUA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-SAM-ribo.tte
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-23.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GCG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.UGA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-38.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CCG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-46.dra
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CGU
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-T-box.bsu
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-23.tth
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-46.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GAG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CAA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-c-di-GMP-II.cac
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-11 (T. thermophilus)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.AUA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GGA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-L30e.sce
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CCA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-7 (T. thermophilus)
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GCA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GUG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-42.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-U4a.hsa
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CUA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.AAG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+.(((((((((.......))))))(.(.((((..((..((((((..........)))))).))..)))).).))))	((((((((((.......))))))(((......)))...)))).(((((...(.((.......)).)....)))))	-6.19940757751
+>SNORD114-4 x Kt-CD-box.GUA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.GGG
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-CD-box.CGA
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-11.eco
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
+>SNORD114-4 x Kt-46.hma
+CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/SNORD118-revised.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD118-revised.fa	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,2 @@
+>SNORD118 revised
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/SNORD118-revised.scan-for-segments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD118-revised.scan-for-segments.txt	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,123 @@
+>SNORD118 x Kt-CD-box.AGA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UAA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-42.dra
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CUG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.AGG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-42.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Loop-E-Motif.bac
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.ACG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.ACA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-G2nA-SAMribo.bsu
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UGG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-42.tth
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UCA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UCG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-7 G2nA SAM riboswitch (H. marismortui)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UAG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GAA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CGG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-15.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CAG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-U4b.hsa
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-7 (E. coli)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-7 (D. radiodurans)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-58.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UUG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-46.tth
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.AUG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UUA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-SAM-ribo.tte
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-23.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GCG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.UGA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-38.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CCG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-46.dra
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CGU
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+.......((.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).))).....))	((.(((.(((((((.(.....)....))...))))(.(((....)))((((((((...........)))))))).)).)))))(....)	-14.319940567
+>SNORD118 x Kt-T-box.bsu
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-23.tth
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-46.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GAG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CAA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-c-di-GMP-II.cac
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-11 (T. thermophilus)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.AUA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GGA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-L30e.sce
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CCA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-7 (T. thermophilus)
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GCA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GUG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-42.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-U4a.hsa
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CUA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.AAG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GUA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.GGG
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-CD-box.CGA
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-11.eco
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
+>SNORD118 x Kt-46.hma
+AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/SNORD13-revised.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD13-revised.fa	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,2 @@
+>SNORD13 revised
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
\ No newline at end of file
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/SNORD13-revised.scan-for-segments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD13-revised.scan-for-segments.txt	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,123 @@
+>SNORD13 x Kt-CD-box.AGA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UAA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-42.dra
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CUG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.AGG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-42.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Loop-E-Motif.bac
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.ACG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.ACA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-G2nA-SAMribo.bsu
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UGG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-42.tth
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UCA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UCG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-7 G2nA SAM riboswitch (H. marismortui)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UAG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GAA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CGG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-15.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CAG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-U4b.hsa
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-7 (E. coli)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-7 (D. radiodurans)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-58.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UUG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-46.tth
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.AUG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UUA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-SAM-ribo.tte
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-23.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GCG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.UGA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-38.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CCG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-46.dra
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CGU
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+(((((.....((.(.(((.(((((.((((((....))))))..((((((........((.(((...))).)).)))))).))))))))).)).)))))	(((((.(.(...((((((.(((((.((((((....))))))..((((((........((.(((...))).)).)))))).))))))))))))))))))	2.15042304993
+>SNORD13 x Kt-T-box.bsu
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-23.tth
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-46.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GAG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CAA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-c-di-GMP-II.cac
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-11 (T. thermophilus)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.AUA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GGA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-L30e.sce
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CCA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-7 (T. thermophilus)
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GCA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GUG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-42.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-U4a.hsa
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CUA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.AAG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GUA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.GGG
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-CD-box.CGA
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-11.eco
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
+>SNORD13 x Kt-46.hma
+GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/SNORD48-revised.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD48-revised.fa	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,2 @@
+>SNORD48 revised (2 extra bases on 5' end)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
\ No newline at end of file
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/SNORD48-revised.scan-for-segments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNORD48-revised.scan-for-segments.txt	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,122 @@
+>SNORD48 x Kt-CD-box.AGA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UAA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-42.dra
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CUG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.AGG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-42.eco
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Loop-E-Motif.bac
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.ACG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.ACA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-G2nA-SAMribo.bsu
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UGU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UGG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-42.tth
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UCA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-G2nA-SAM-riboswitch (T. tengcongensi)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UCG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-7 G2nA SAM riboswitch (H. marismortui)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UAG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GAA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CGG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-15.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CAG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-U4b.hsa
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-7 (E. coli)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-7 (D. radiodurans)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-58.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UUG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-46.tth
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.AUG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UUA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-SAM-ribo.tte
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-23.eco
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GCG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.UGA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-38.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CCG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-46.dra
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CGU
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-T-box.bsu
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-23.tth
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-46.eco
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GAG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CAA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-c-di-GMP-II.cac
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-11 (T. thermophilus)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.AUA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GGA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-L30e.sce
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CCA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-7 (T. thermophilus)
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GCA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GUG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-42.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-U4a.hsa
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CUA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.AAG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GUA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.GGG
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-CD-box.CGA
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-11.eco
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
+>SNORD48 x Kt-46.hma
+GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/segments_truncated.out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments_truncated.out.txt	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,4 @@
+>C/D-box snoRNA (shuffle iteration 1)
+cgCGUGAUgagUGAgucagagcacc
+>Artificial double C/D K-turn construct (shuffle iteration 1)
+ggcauuaccgacaguccucguaacaggaauaucguacggucUGUGAUaUGAuuucaucguggaacuuUGUGAUcggcgggauUGA
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/segments_truncated.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments_truncated.xml	Mon Feb 29 10:43:37 2016 -0500
@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<root>
+	<segments>
+		<segment>
+			<id>Kt-CD-box.UGU</id><!-- Common -->
+			<sequence_5prime>UGUGAU</sequence_5prime>
+			<bonds          >   :::</bonds>
+			<sequence_3prime>   AGU</sequence_3prime>
+			<energy>-11.1072</energy>
+			<directions>
+				<five_prime>true</five_prime>
+				<three_prime>true</three_prime>
+			</directions>
+		</segment>
+		
+		<segment>
+			<id>Kt-CD-box.CGU</id><!-- Common -->
+			<sequence_5prime>CGUGAU</sequence_5prime>
+			<bonds          >   :::</bonds>
+			<sequence_3prime>   AGU</sequence_3prime>
+			<energy>-11.1072</energy>
+			<directions>
+				<five_prime>true</five_prime>
+				<three_prime>true</three_prime>
+			</directions>
+		</segment>
+	</segments>
+	
+	
+	<segmentloops />
+	
+	
+	<!-- RNA-Molecules -->
+	<rnas>
+		<rna>
+			<title>C/D-box snoRNA</title>
+			<organism>A. fulgidus</organism>
+			<sequence>GCUCUGACCGAAAGGCGUGAUGAGC</sequence>
+			
+			<structures>
+				<structure>
+					<associated_segments>
+						<link>Kt-CD-box.CGU</link>
+					</associated_segments>
+					<dot_bracket type="full"   >(((((((((....))...)))))))</dot_bracket>
+				</structure>
+				
+				<structure>
+					<associated_segments />
+					<dot_bracket />
+				</structure>
+			</structures>
+			
+			<references>
+				<pdb>1RLG</pdb>
+				<url>http://www.sciencedirect.com/science/article/pii/S0969212604001169</url>
+			</references>
+		</rna>
+		
+		<rna>
+			<title>Artificial double C/D K-turn construct</title>
+			<sequence>GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC</sequence>
+			
+			<structures>
+				<structure>
+					<associated_segments>
+						<link>Kt-CD-box.UGU</link>
+					</associated_segments>
+					<dot_bracket type="full"   >((((((((...((((?????????????((((((((((((.....))))))))...))))?????????????))))))))))))</dot_bracket>
+				</structure>
+				
+				<structure>
+					<associated_segments />
+					<dot_bracket />
+				</structure>
+			</structures>
+			
+			<references>
+				<pdb>3ICX</pdb>
+				<pdb>3ID6</pdb>
+				<doi>http://dx.doi.org/10.1038/nature09688</doi>
+			</references>
+		</rna>
+	</rnas>
+</root>
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_02.dbn
--- a/test-data/test_02.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_02.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 34bp, dE: -34.4572 kcal/mole
 CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG
-((((((((((((..(...))))...)))))))))
+((((((((((((.......)))...)))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_03.dbn
--- a/test-data/test_03.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_03.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 35bp, dE: -31.2572 kcal/mole
 CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG
-((((((((((((..(...)))))....))))))))
+((((((((((((.......))))....))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_05.dbn
--- a/test-data/test_05.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_05.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 47bp, dE: -42.9072 kcal/mole
+>Sequence length: 47bp, dE: -42.5072 kcal/mole
 CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG
-((((.(((((..(((((.((((....))))))))))))...))))))
+((((.(((((..((((((((.......)))))))))))...))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_06.dbn
--- a/test-data/test_06.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_06.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 47bp, dE: -41.3572 kcal/mole
+>Sequence length: 47bp, dE: -40.3572 kcal/mole
 GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC
-((((.(((((..((((((.(((....))))))))))))...))))))
+((((.(((((..((((((((.......)))))))))))...))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_07.dbn
--- a/test-data/test_07.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_07.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 31bp, dE: -28.7072 kcal/mole
+>Sequence length: 31bp, dE: -26.5072 kcal/mole
 AACCGAAGCCCUCACGGGCAAUGUGGUGUCA
-.((((.(((((....))))...)))))....
+..(((.(((((....))))...)))).....
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_08.dbn
--- a/test-data/test_08.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_08.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 37bp, dE: -33.7572 kcal/mole
 UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG
-((((((((((((((.(...))))...)))))))))))
+((((((((((((((......)))...)))))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_09.dbn
--- a/test-data/test_09.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_09.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 37bp, dE: -30.8072 kcal/mole
 UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG
-((((((((((((((.(...))))...)))))))))))
+((((((((((((((......)))...)))))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_10.dbn
--- a/test-data/test_10.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_10.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 109bp, dE: -82.9072 kcal/mole
+>Sequence length: 109bp, dE: -76.7072 kcal/mole
 CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG
-((((((((((((.(((((((((((.((((.(((....))))).)).))))).(((.(((((.((((....))))..)))))...))))))))))))....)))))))))
+((((((((((((.(((((((((...(((.(((..(..((((((.(((.((((....)))).)))))))))))))...)))....))))))))))))....)))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_11.dbn
--- a/test-data/test_11.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_11.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -49.0072 kcal/mole
+>Sequence length: 53bp, dE: -46.6072 kcal/mole
 GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC
-(((.((((((((((...((.((((((......)))))))))))))))))))))
+((((.(((((((((...((.((((((......)))))))))))))))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_12.dbn
--- a/test-data/test_12.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_12.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -51.5072 kcal/mole
+>Sequence length: 53bp, dE: -50.2072 kcal/mole
 GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC
 ((.(((((((((((...((.((((((......)))))))))))))))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_13.dbn
--- a/test-data/test_13.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_13.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -44.8072 kcal/mole
+>Sequence length: 53bp, dE: -43.5072 kcal/mole
 GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC
 ((.(((((((((((...((.((((((......)))))))))))))))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_14.dbn
--- a/test-data/test_14.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_14.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 53bp, dE: -39.2072 kcal/mole
+>Sequence length: 53bp, dE: -37.9072 kcal/mole
 CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG
 ((.((..((..(((...((.((((((......)))))))))))..))..))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_16.dbn
--- a/test-data/test_16.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_16.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 50bp, dE: -44.4072 kcal/mole
+>Sequence length: 50bp, dE: -43.4072 kcal/mole
 UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA
-(((((..((((...((((((((.((.....)))))))))))))).)))))
+(((((...(((...((((((((..((....)))))))))))))..)))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_17.dbn
--- a/test-data/test_17.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_17.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 49bp, dE: -38.8072 kcal/mole
+>Sequence length: 49bp, dE: -37.3072 kcal/mole
 UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA
 (((((((.((...((((((((.((....)).)))))))))).)))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_18.dbn
--- a/test-data/test_18.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_18.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
 >Sequence length: 50bp, dE: -37.7072 kcal/mole
 UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA
-(((((.(.(((...(((((((((((....)))))))))))))).))))))
+(((((...(((...(((((((((((....))))))))))))))..)))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_19.dbn
--- a/test-data/test_19.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_19.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 30bp, dE: -29.8572 kcal/mole
+>Sequence length: 30bp, dE: -28.4572 kcal/mole
 UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA
-((((((((.((((...))))..))))))))
+((((((((.(((.....)))..))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_21.dbn
--- a/test-data/test_21.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_21.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 34bp, dE: -30.6072 kcal/mole
+>Sequence length: 34bp, dE: -27.7072 kcal/mole
 ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU
 (((((.(((...(((((....)))))))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_23.dbn
--- a/test-data/test_23.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_23.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 85bp, dE: -70.7144 kcal/mole
+>Sequence length: 85bp, dE: -70.4144 kcal/mole
 GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC
-((((((((...(((((((.((...(..(((((((((((((.....))))))))...)))))..)))))....)))))))))))))
+((((((((...(((((..(((......(((((((((((((.....))))))))...)))))...))).....)))))))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 test-data/test_26.dbn
--- a/test-data/test_26.dbn	Wed Dec 02 04:34:50 2015 -0500
+++ b/test-data/test_26.dbn	Mon Feb 29 10:43:37 2016 -0500
@@ -1,3 +1,3 @@
->Sequence length: 55bp, dE: -43.9072 kcal/mole
+>Sequence length: 55bp, dE: -42.1072 kcal/mole
 GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC
 ((((((...(((((((....(((((((....))))...))).)))))))))))))
diff -r eccb5ee89df7 -r 59ab674be4b5 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 02 04:34:50 2015 -0500
+++ b/tool_dependencies.xml	Mon Feb 29 10:43:37 2016 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="segmentation-fold" version="1.1.0">
-        <repository changeset_revision="fba0d6f9dd67" name="package_segmentation_fold_1_1_0" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="segmentation-fold" version="1.6.0">
+        <repository changeset_revision="5b89079b53e2" name="package_segmentation_fold_1_6_0" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>