Mercurial > repos > yhoogstrate > segmentation_fold
changeset 2:22d7b6019372 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 7e54643d9af0065268d5cde2f2fc9872d2de8fa9
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--- a/README.rst Thu Dec 03 03:22:08 2015 -0500 +++ b/README.rst Thu Mar 31 04:16:21 2016 -0400 @@ -5,6 +5,11 @@ Segmentation-fold: An algorithm for predicting RNA 2D structures including K-turns +Installation +------------ + +Requires a C++11 compliant compiler! + Development -----------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/energy-estimation-utility.xml Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,111 @@ +<tool id="energy_estimation_utility" name="energy-estimation-utility" version="1.6.3-0"> + <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="1.6.3">segmentation-fold</requirement> + <requirement type="package" version="2.7.10">python</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="${tool.name}" /> + </outputs> + + <tests> + <test> + <param name="use_custom_xml" value="true" /> + <param name="input_xml" value="segments_truncated.xml" ftype="xml" /> + <param name="do_randomization" value="false" /> + <param name="shuffle_n_times" value="0" /> + + <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" /><!-- Accept rounding errors by diff CPU's etc. --> + </test> + <test> + <param name="use_custom_xml" value="true" /> + <param name="input_xml" value="segments_truncated.xml" ftype="xml" /> + <param name="do_randomization" value="false" /> + <param name="shuffle_n_times" value="1" /> + + <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" /> + </test> + </tests> + + <help><![CDATA[ +The tool uses the sequences from the xml file. + ]]></help> + + <citations> + <citation type="bibtex"> + @mastersthesis{mastersthesis, + author = {Youri Hoogstrate}, + title = {An algorithm for predicting RNA 2D structures including K-turns}, + school = {University of Technology Delft, Leiden University}, + year = 2012, + address = {}, + month = 11, + note = {Research assignment for Master Computer-science}, + url = { https://yh-kt-fold.googlecode.com/files/Report.pdf } + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scan-for-segments.xml Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,105 @@ +<tool id="scan_for_segments" name="scan-for-segments" version="1.6.3-0"> + <description>Scan for the presence of segments in sequences using segmentation-fold</description> + + <requirements> + <requirement type="package" version="1.6.3">segmentation-fold</requirement> + <requirement type="package" version="2.7.10">python</requirement> + </requirements> + + <stdio></stdio> + + <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command> + + <command><![CDATA[ + scan-for-segments + -T \${GALAXY_SLOTS:-4} + -x + #if str($parameters.use_custom_xml) == "true" + "${parameters.input_xml}" + #else + "\$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>
--- a/segmentation-fold.xml Thu Dec 03 03:22:08 2015 -0500 +++ b/segmentation-fold.xml Thu Mar 31 04:16:21 2016 -0400 @@ -1,8 +1,8 @@ -<tool id="segmentation_fold" name="segmentation-fold" version="1.1.0_1"> +<tool id="segmentation_fold" name="segmentation-fold" version="1.6.3-0"> <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="1.6.3">segmentation-fold</requirement> </requirements> <stdio></stdio> @@ -61,7 +61,7 @@ </inputs> <outputs> - <data format="dot-bracket" name="output_dbn" label="asdasdasd" /> + <data format="dbn" name="output_dbn" label="segmentation-fold" /> <!--<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> @@ -181,16 +181,57 @@ </tests> <help><![CDATA[ -Segmentation-fold is a bioinformatics application that predicts RNA -2D-structure with an extended version of the Zuker algorithm. This -modification contains a new "structure element" named a segment and is -capable of folding a pre-defined substructures with multiple canonical -or non-canonical pairings. +**What it does**: + +Segmentation-fold is a application in the field of bioinformatics that +predicts RNA 2D-structures. The model has an extension with respect to +the classical Zuker algorithm, to allow new "structure elements" named +segments and segmentloops. This makes it capable of folding a +pre-defined substructure with multiple canonical or non-canonical base +pairs, like K-turns and loop-E-motifs. Some of such sturcture elements +are present in the corresponding energy table, although custom tables +can be provided as well. + + +**Running segmentation-fold** + +Segmentation-fold has to be provided with a sequence of which it has to +predict the 2D structure. This can be done using a plain text sequence +(allowed charset: ACTUG) or a FASTA file. A FASTA file has the following +syntax: + + >Sequence name and other details + + AGUGUAGCUGUGUCGAUCGUAAGUCAG -This allows folding of more complex structures like K-turns, which are -also part of the implemented free energy table. These thermodynamic -parameters (free Gibbs energy) have been estimated using a in silico -approach and therefore lack high resolution. +As the database of free energy parameters will most likely be updated +over time we have added the possiblity to include this XML file as +additional parameter. The most up to date version of this file can be +found at the following url: + +https://github.com/yhoogstrate/segmentation-fold/blob/master/share/segmentation-fold/segments.xml + +If you would like to compare the results with a prediction as if the +segment and segmentloop extension were disabled, you can disable it with +the given parameter. + +**Output** + +The output is in DotBracket format (dbn) and can be visualized with e.g. +DrawRNAjs or VaRNA. + +DrawRNAjs can be installed in galaxy by following the instructions at +the following link: + +https://github.com/bgruening/galaxytools/tree/master/visualisations/drawrnajs + +Details on the dbn-format can be found here: + +https://wiki.galaxyproject.org/Learn/Datatypes#Dbn + +**Authors** + +Youri Hoogstrate (yhoogstrate @ github) ]]></help> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD114-4-revised.fa Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,2 @@ +>SNORD114-4 revised +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD114-4-revised.scan-for-segments.txt Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,74 @@ +>SNORD114-4 x Kt-42.dra +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-42.eco +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Loop-E-Motif.bac +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-CD-box.UAU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-CD-box.UGU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-CD-box.CAU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-42.tth +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-7 G2nA SAM riboswitch (H. marismortui) +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-15.hma +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..))))) .((((((....(((.((.....((((......))))((....))...)...))))...(((....))).)))))) -6.4197063446 +>SNORD114-4 x Kt-U4b.hsa +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-CD-box.GGU +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-46.tth +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-SAM-ribo.tte +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-23.eco +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-38.hma +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-c-di-GMP-II.cac +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-11 (T. thermophilus) +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-CD-box.AAU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-L30e.sce +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-7 (T. thermophilus) +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-42.hma +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-U4a.hsa +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-G2nA-SAMribo.bsu +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-CD-box.GAU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-11.eco +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-46.hma +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 x Kt-CD-box.AGU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..))))) .((((((...(((((.......((((......)))).((((((..........)))))).....))))))))))) 1.99971199036
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD118-revised.fa Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,2 @@ +>SNORD118 revised +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD118-revised.scan-for-segments.txt Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,75 @@ +>SNORD118 x Kt-42.dra +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-42.eco +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Loop-E-Motif.bac +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-CD-box.UAU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-CD-box.UGU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-CD-box.CAU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) .(((...((((((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).))))))))). 3.380651474 +>SNORD118 x Kt-42.tth +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-7 G2nA SAM riboswitch (H. marismortui) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-15.hma +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-U4b.hsa +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-CD-box.GGU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-7 (E. coli) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-7 (D. radiodurans) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-58.hma +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-46.tth +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-SAM-ribo.tte +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-23.eco +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-38.hma +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-46.dra +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-CD-box.CGU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) (((((...((((((............))...))))...))......(((((((((...........))))))))).....)))...... -15.021024704 +>SNORD118 x Kt-T-box.bsu +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-23.tth +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-46.eco +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-c-di-GMP-II.cac +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-11 (T. thermophilus) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-CD-box.AAU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-L30e.sce +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-7 (T. thermophilus) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-42.hma +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-U4a.hsa +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-G2nA-SAMribo.bsu +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-CD-box.GAU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) (((.(((...(((((......))))))((((.....))))...)).(((((((((...........))))))))).....)))...... -8.30012321472 +>SNORD118 x Kt-11.eco +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-46.hma +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 x Kt-CD-box.AGU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD13-revised.fa Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,2 @@ +>SNORD13 revised +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD13-revised.scan-for-segments.txt Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,74 @@ +>SNORD13 x Kt-42.dra +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-42.eco +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Loop-E-Motif.bac +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-CD-box.UAU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-CD-box.UGU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-CD-box.CAU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-42.tth +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-7 G2nA SAM riboswitch (H. marismortui) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-15.hma +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-U4b.hsa +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-CD-box.GGU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-7 (E. coli) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-7 (D. radiodurans) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-58.hma +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-46.tth +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-SAM-ribo.tte +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-23.eco +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-38.hma +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-46.dra +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-CD-box.CGU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..)))))) (((((.(.(...((((((.((((((((((((....)))))))(((((((..(.((((((...))).))).)..))))))))))))))))))))))))) 3.35026359558 +>SNORD13 x Kt-T-box.bsu +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-23.tth +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-46.eco +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-c-di-GMP-II.cac +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-11 (T. thermophilus) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-CD-box.AAU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-L30e.sce +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-7 (T. thermophilus) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-42.hma +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-U4a.hsa +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-G2nA-SAMribo.bsu +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-CD-box.GAU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..)))))) (((((((.((((...((((((((((....))))))..)))))...)))))............((((.((((.((........)))))))))).))))) -9.91994667053 +>SNORD13 x Kt-11.eco +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-46.hma +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 x Kt-CD-box.AGU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD48-revised.fa Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,2 @@ +>SNORD48 revised (2 extra bases on 5' end) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD48-revised.scan-for-segments.txt Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,74 @@ +>SNORD48 x Kt-42.dra +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-42.eco +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Loop-E-Motif.bac +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-CD-box.UAU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-CD-box.UGU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-CD-box.CAU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-42.tth +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-7 G2nA SAM riboswitch (H. marismortui) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-15.hma +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-U4b.hsa +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-CD-box.GGU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-7 (E. coli) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-7 (D. radiodurans) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-58.hma +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-46.tth +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-SAM-ribo.tte +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-23.eco +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-38.hma +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-c-di-GMP-II.cac +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-11 (T. thermophilus) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-CD-box.AAU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-L30e.sce +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-7 (T. thermophilus) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-42.hma +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-U4a.hsa +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-G2nA-SAMribo.bsu +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-CD-box.GAU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +((((((.((.((((((((((.....)))).).).)))).((((...))))...)).)))))).... (((((...(((((((...))).....))))).....(((((............))))))))).... -10.9206504822 +>SNORD48 x Kt-11.eco +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-46.hma +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 x Kt-CD-box.AGU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +((((((.((.((((((((((.....)))).).).)))).((((...))))...)).)))))).... ((...(((((..((..((((.....)))).))((((.((((((...))))..)).))))))))))) -1.84962844849
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/segments_truncated.2.out.txt Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,5 @@ +>C/D-box snoRNA (shuffle iteration 1) +agaggCGUGAUcccaacgUGAuggc +....((((.......))))...... ....(...((((.....)))))... -9.3900680542 +>Artificial double C/D K-turn construct (shuffle iteration 1) +uguucugucacggcacauaccuccggUGUGAUggUGAauaguaUGAgaaguaucgugugucagaggcccuaaUGUGAUgccuuaa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/segments_truncated.out.txt Thu Mar 31 04:16:21 2016 -0400 @@ -0,0 +1,6 @@ +>C/D-box snoRNA +GCUCUGACCGAAAGGCGUGAUGAGC +((((....((.....))....)))) (((((((((....))...))))))) 2.50072479248 +>Artificial double C/D K-turn construct +GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC +((((((((((((........))).((((((((((((((((.....))))))))(((......))).))).))))).))))))))) ((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..))))))))))))) -1.25102996826
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/segments_truncated.xml Thu Mar 31 04:16:21 2016 -0400 @@ -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>
--- a/test-data/test_01.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_01.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 34bp, dE: -32.2572 kcal/mole +>Sequence length: 34bp, dE: -28.56 kcal/mole, segments: 1 CCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGG ((((((((((((.......)))...)))))))))
--- a/test-data/test_02.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_02.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 34bp, dE: -34.4572 kcal/mole +>Sequence length: 34bp, dE: -30.16 kcal/mole, segments: 1 CCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGG ((((((((((((.......)))...)))))))))
--- a/test-data/test_03.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_03.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 35bp, dE: -31.2572 kcal/mole +>Sequence length: 35bp, dE: -26.76 kcal/mole, segments: 1 CGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCG ((((((((((((.......))))....))))))))
--- a/test-data/test_04.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_04.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 34bp, dE: -30.4872 kcal/mole +>Sequence length: 34bp, dE: -23.19 kcal/mole, segments: 1 CCCCGACGAGCUGGAGAUACCCUUUGACUCGGGG ((((((((((..((.....)))...)))))))))
--- a/test-data/test_05.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_05.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 47bp, dE: -42.5072 kcal/mole +>Sequence length: 47bp, dE: -34.71 kcal/mole, segments: 1 CCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGG ((((.(((((..((((((((.......)))))))))))...))))))
--- a/test-data/test_06.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_06.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 47bp, dE: -40.3572 kcal/mole +>Sequence length: 47bp, dE: -32.56 kcal/mole, segments: 1 GGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCC ((((.(((((..((((((((.......)))))))))))...))))))
--- a/test-data/test_07.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_07.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 31bp, dE: -26.5072 kcal/mole +>Sequence length: 31bp, dE: -24.51 kcal/mole, segments: 1 AACCGAAGCCCUCACGGGCAAUGUGGUGUCA -..(((.(((((....))))...))))..... +.((((.(((((....))))...)))))....
--- a/test-data/test_08.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_08.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 37bp, dE: -33.7572 kcal/mole +>Sequence length: 37bp, dE: -29.26 kcal/mole, segments: 1 UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAG ((((((((((((((......)))...)))))))))))
--- a/test-data/test_09.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_09.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 37bp, dE: -30.8072 kcal/mole +>Sequence length: 37bp, dE: -26.31 kcal/mole, segments: 1 UUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAG ((((((((((((((......)))...)))))))))))
--- a/test-data/test_10.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_10.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 109bp, dE: -76.7072 kcal/mole +>Sequence length: 109bp, dE: -66.21 kcal/mole, segments: 1 CUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGG -((((((((((((.(((((((((...(((.(((..(..((((((.(((.((((....)))).)))))))))))))...)))....))))))))))))....))))))))) +((((((((((((.(((((((((...(((.....(((.((((((.(((.((((....)))).))))))))).)))...)))....))))))))))))....)))))))))
--- a/test-data/test_11.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_11.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 53bp, dE: -46.6072 kcal/mole +>Sequence length: 53bp, dE: -42.71 kcal/mole, segments: 1 GGUGGUCUCGAGCCCUAGACAGCCGGUUUUUUCCGGCCGAGGUUUGAGGCGCC ((((.(((((((((...((.((((((......)))))))))))))))))))))
--- a/test-data/test_12.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_12.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 53bp, dE: -50.2072 kcal/mole +>Sequence length: 53bp, dE: -46.31 kcal/mole, segments: 1 GGAUGUGGCGCCGCGAAGACAGCCAGUUUUUUCUGGUCGAGUGGCGCCGCGCC ((.(((((((((((...((.((((((......)))))))))))))))))))))
--- a/test-data/test_13.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_13.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 53bp, dE: -43.5072 kcal/mole +>Sequence length: 53bp, dE: -39.61 kcal/mole, segments: 1 GGAUGUGUCGUCGCAUAGACAGCCAGUUUUUUCUGGUCGAGUGACGAUGCGCC ((.(((((((((((...((.((((((......)))))))))))))))))))))
--- a/test-data/test_14.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_14.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 53bp, dE: -37.9072 kcal/mole +>Sequence length: 53bp, dE: -34.01 kcal/mole, segments: 1 CGAUGUGGGAAGGCCCAGACAGCCAGUUUUUUCUGGUCGAGUCGGCCUGCGCG ((.((..((..(((...((.((((((......)))))))))))..))..))))
--- a/test-data/test_15.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_15.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 49bp, dE: -37.8572 kcal/mole +>Sequence length: 49bp, dE: -32.16 kcal/mole, segments: 1 CUCUAAUUGGAUGGAAGUAGGGGUGAAAACUCCUAUGGACCGAUUAGUG (.((((((((...(((((((((((....))))))))))))))))))).)
--- a/test-data/test_16.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_16.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 50bp, dE: -43.4072 kcal/mole +>Sequence length: 50bp, dE: -34.51 kcal/mole, segments: 1 UUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGCGGCUGGAGGUAAGGGAA -(((((...(((...((((((((..((....)))))))))))))..))))) +(((((..((((...((((((((.((.....)))))))))))))).)))))
--- a/test-data/test_17.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_17.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 49bp, dE: -37.3072 kcal/mole +>Sequence length: 49bp, dE: -30.91 kcal/mole, segments: 1 UUCAGUCCGCGGUGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAA (((((((.((...((((((((.((....)).)))))))))).)))))))
--- a/test-data/test_18.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_18.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 50bp, dE: -37.7072 kcal/mole +>Sequence length: 50bp, dE: -30.61 kcal/mole, segments: 1 UUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAA (((((...(((...(((((((((((....))))))))))))))..)))))
--- a/test-data/test_19.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_19.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 30bp, dE: -28.4572 kcal/mole +>Sequence length: 30bp, dE: -24.46 kcal/mole, segments: 1 UCCGUGGAAGCCGUAAUGGCAGGAAGCGGA -((((((((.(((.....)))..)))))))) +((((((((.((((...))))..))))))))
--- a/test-data/test_20.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_20.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 22bp, dE: -23.2072 kcal/mole +>Sequence length: 22bp, dE: -19.11 kcal/mole, segments: 1 GCCAAUGAGGUUUAUCCGAGGC (((...((((.....)))))))
--- a/test-data/test_21.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_21.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 34bp, dE: -27.7072 kcal/mole +>Sequence length: 34bp, dE: -22.71 kcal/mole, segments: 1 ACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGU (((((.(((...(((((....)))))))))))))
--- a/test-data/test_22.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_22.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 25bp, dE: -24.4072 kcal/mole +>Sequence length: 25bp, dE: -18.01 kcal/mole, segments: 1 GCUCUGACCGAAAGGCGUGAUGAGC (((((((((....))...)))))))
--- a/test-data/test_23.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_23.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 85bp, dE: -70.4144 kcal/mole +>Sequence length: 85bp, dE: -60.91 kcal/mole, segments: 2 GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC -((((((((...(((((..(((......(((((((((((((.....))))))))...)))))...))).....))))))))))))) +((((((((...(((((..(....((..(((((((((((((.....))))))))...)))))..))....)..)))))))))))))
--- a/test-data/test_24.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_24.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 34bp, dE: -29.0072 kcal/mole +>Sequence length: 34bp, dE: -25.41 kcal/mole, segments: 1 GGACGCAGAGAUGGUCUUUUUGACCGGAGUGUCC ((((((...(((((((.....)))))))))))))
--- a/test-data/test_25.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_25.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 26bp, dE: -24.7072 kcal/mole +>Sequence length: 26bp, dE: -20.41 kcal/mole, segments: 1 GGUGGAGGGACUGGCCCGAUGAAACC (((((((((.....)))...))))))
--- a/test-data/test_26.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_26.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 55bp, dE: -42.1072 kcal/mole +>Sequence length: 55bp, dE: -33.71 kcal/mole, segments: 1 GGGAGUAAAGAUUGAGACAAGUAGGACUUCGGUCCGAAUACACUCAUGAACUCCC -((((((...(((((((....(((((((....))))...))).))))))))))))) +((((((...(((((((...(((...)))(((...))).....)))))))))))))
--- a/test-data/test_27.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_27.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 36bp, dE: -26.2072 kcal/mole +>Sequence length: 36bp, dE: -22.71 kcal/mole, segments: 1 AACAAUGAUGAAUGGGUUUUUUACUCAUUUUGAGUU (((...(((((((((((.....))))))))))))))
--- a/test-data/test_28.dbn Thu Dec 03 03:22:08 2015 -0500 +++ b/test-data/test_28.dbn Thu Mar 31 04:16:21 2016 -0400 @@ -1,3 +1,3 @@ ->Sequence length: 26bp, dE: -24.7072 kcal/mole +>Sequence length: 26bp, dE: -20.41 kcal/mole, segments: 1 GGUGAAGGGACUGGCCCGACGAAACC (((((((((.....)))...))))))
--- a/tool_dependencies.xml Thu Dec 03 03:22:08 2015 -0500 +++ b/tool_dependencies.xml Thu Mar 31 04:16:21 2016 -0400 @@ -1,6 +1,10 @@ <?xml version="1.0"?> <tool_dependency> - <package name="segmentation-fold" version="1.1.0"> - <repository changeset_revision="2c69127ea0cd" name="package_segmentation_fold_1_1_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="segmentation-fold" version="1.6.3"> + <repository changeset_revision="a6b5d3d4825c" name="package_segmentation_fold_1_6_3" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="python" version="2.7.10"> + <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>