| Previous changeset 1:ec0fdb8c4ebb (2015-02-04) Next changeset 3:04c56f5b0907 (2015-02-13) |
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Commit message:
Uploaded |
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modified:
rna2dfold.xml rnaaliduplex.xml rnaalifold.xml rnacofold.xml rnadistance.xml rnaduplex.xml rnaeval.xml rnafold.xml rnaheat.xml rnainverse.xml rnalalifold.xml rnalfold.xml rnapaln.xml rnapdist.xml rnapkplex.xml rnaplex.xml rnaplfold.xml rnaplot.xml rnasnoop.xml rnasubopt.xml rnaup.xml tool_dependencies.xml |
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added:
test-data/rna2dfold_input1.txt test-data/rna2dfold_result1.txt test-data/rnaaliduplex_input1.clustal test-data/rnaaliduplex_result1.txt test-data/rnaalifold_input1.clustal test-data/rnaalifold_result1.txt test-data/rnacofold_input1.fas test-data/rnacofold_result1.txt test-data/rnadistance_input1.fas test-data/rnadistance_result1.txt test-data/rnaduplex_input1.fa test-data/rnaduplex_result1.txt test-data/rnaeval_input1.fas test-data/rnaeval_result1.txt test-data/rnafold_input1.fa test-data/rnafold_input2.fa test-data/rnafold_output1.tar test-data/rnafold_result1.txt test-data/rnafold_result2.txt test-data/rnaheat_input1.fa test-data/rnaheat_result1.txt test-data/rnainverse_input1.fas test-data/rnalalifold_input1.clustal test-data/rnalalifold_result1.txt test-data/rnalfold_input1.fa test-data/rnalfold_result1.txt test-data/rnapaln_input1.fa test-data/rnapaln_input1.fas test-data/rnapaln_result1.txt test-data/rnapdist_input1.fa test-data/rnapdist_result1.txt test-data/rnapkplex_input1.fa test-data/rnapkplex_result1.txt test-data/rnaplex_input1.fa test-data/rnaplex_result1.txt test-data/rnaplfold_input1.fa test-data/rnaplfold_result1.txt test-data/rnaplot_input1.fa test-data/rnaplot_input1.fas test-data/rnasnoop_input1a.fa test-data/rnasnoop_input1b.fa test-data/rnasnoop_result1.txt test-data/rnasubopt_input1.fa test-data/rnasubopt_result1.txt test-data/rnaup_input1.fa test-data/rnaup_result1.txt |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rna2dfold.xml --- a/rna2dfold.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rna2dfold.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -78,6 +78,11 @@ <data format="txt" name="out_file"/> </outputs> <tests> + <test> + <param name="custom_input" value="rna2dfold_input1.txt"/> + <param name="nrbt" value="0"/> + <output name="out_file1" file="rna2dfold_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaaliduplex.xml --- a/rnaaliduplex.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaaliduplex.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -51,6 +51,11 @@ <data format="txt" name="out_file"/> </outputs> <tests> + <test> + <param name="input1" value="rnaaliduplex_input1.clustal"/> + <param name="input2" value="rnaaliduplex_input1.clustal"/> + <output name="out_file1" file="rnaaliduplex_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaalifold.xml --- a/rnaalifold.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaalifold.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -93,6 +93,10 @@ <data format="tar" name="imagesFile"/> </outputs> <tests> + <test> + <param name="input" value="rnaalifold_input1.clustal"/> + <output name="output" file="rnaalifold_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnacofold.xml --- a/rnacofold.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnacofold.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -62,6 +62,10 @@ </collection> </outputs> <tests> + <test> + <param name="input" value="rnacofold_input1.fas"/> + <output name="out_file" file="rnacofold_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnadistance.xml --- a/rnadistance.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnadistance.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -46,6 +46,10 @@ <data format="txt" name="outfile"/> </outputs> <tests> + <test> + <param name="input" value="rnadistance_input1.fas"/> + <output name="outfile" file="rnadistance_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaduplex.xml --- a/rnaduplex.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaduplex.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -51,6 +51,10 @@ <data format="txt" name="tabularFile"/> </outputs> <tests> + <test> + <param name="input" value="rnaduplex_input1.fa"/> + <output name="out_file" file="rnaduplex_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaeval.xml --- a/rnaeval.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaeval.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -51,6 +51,10 @@ <data format="txt" name="tabularFile"/> </outputs> <tests> + <test> + <param name="input" value="rnaeval_input1.fas"/> + <output name="out_file" file="rnaeval_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnafold.xml --- a/rnafold.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnafold.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -78,6 +78,15 @@ </outputs> <tests> + <test> + <param name="fasta_input" value="rnafold_input1.fa"/> + <output name="out_file1" file="rnafold_result1.txt"/> + </test> + <test> + <param name="fasta_input" value="rnafold_input2.fa"/> + <param name="temperature" value="75"/> + <output name="out_file1" file="rnafold_result2.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaheat.xml --- a/rnaheat.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaheat.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -52,6 +52,10 @@ <data format="txt" name="output"/> </outputs> <tests> + <test> + <param name="input" value="rnaheat_input1.fa"/> + <output name="out_file" file="rnaheat_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnainverse.xml --- a/rnainverse.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnainverse.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -57,6 +57,14 @@ <data format="txt" name="outfile"/> </outputs> <tests> + <test> + <param name="input" value="rnainverse_input1.fas"/> + <output name="outfile"> + <assert_contents> + <has_line_matching expression="^gggccccnnaauun.*"/> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnalalifold.xml --- a/rnalalifold.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnalalifold.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -24,7 +24,6 @@ --nfactor=$advancedOptions.nfactor $advancedOptions.ribosum #end if - <!--; tar -cf $imagesFile *.ps --> ]]> </command> @@ -68,6 +67,10 @@ <!--<data format="tar" name="imagesFile" label="RNALalifold images"/>--> </outputs> <tests> + <test> + <param name="input" value="rnalalifold_input1.clustal"/> + <output name="output" file="rnalalifold_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnalfold.xml --- a/rnalfold.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnalfold.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -61,6 +61,10 @@ <data format="txt" name="out_file"/> </outputs> <tests> + <test> + <param name="fasta_input" value="rnalfold_input1.fa"/> + <output name="out_file" file="rnalfold_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnapaln.xml --- a/rnapaln.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnapaln.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -78,6 +78,10 @@ </collection> </outputs> <tests> + <test> + <param name="input" value="rnapaln_input1.fa"/> + <output name="out_file" file="rnapaln_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnapdist.xml --- a/rnapdist.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnapdist.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -62,12 +62,16 @@ </inputs> <outputs> <data format="txt" name="output"/> - <data format="txt" name="dotplot"> + <data format="txt" name="dotplot"/> <collection name="matrix_outputs" type="list" label="rna_eps outputs"> <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> </collection> </outputs> <tests> + <test> + <param name="input" value="rnapdist_input1.fa"/> + <output name="out_file" file="rnapdist_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnapkplex.xml --- a/rnapkplex.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnapkplex.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -54,6 +54,10 @@ </collection> </outputs> <tests> + <test> + <param name="input" value="rnapkplex_input1.fa"/> + <output name="out_file" file="rnapkplex_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaplex.xml --- a/rnaplex.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaplex.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -98,6 +98,10 @@ <data format="txt" name="output"/> </outputs> <tests> + <test> + <param name="input" value="rnaplex_input1.fa"/> + <output name="out_file" file="rnaplex_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaplfold.xml --- a/rnaplfold.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaplfold.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -78,6 +78,10 @@ <data format="tar" name="outputf"/> </outputs> <tests> + <test> + <param name="input" value="rnaplfold_input1.fa"/> + <output name="out_file" file="rnaplfold_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaplot.xml --- a/rnaplot.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaplot.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -49,6 +49,14 @@ <data format="tar" name="imagesFile"/> </outputs> <tests> + <test> + <param name="input" value="rnaplot_input1.fas"/> + <output name="imagesFile"> + <assert_contents> + <has_line line="%%Title: RNA Secondary Structure Plot"/> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnasnoop.xml --- a/rnasnoop.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnasnoop.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -10,7 +10,7 @@ <command> <![CDATA[ RNAsnoop --query=$input1 --target=$input2 > $output - --alignmentLenght=$length + --alignmentLength=$length $constraint --energy-threshold=$energyThreshold #if $varExists('$advancedOptions.extensioncost') @@ -99,6 +99,11 @@ </outputs> <tests> + <test> + <param name="input1" value="rnasnoop_input1b.fa"/> + <param name="input2" value="rnasnoop_input1a.fa"/> + <output name="output" file="rnasnoop_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnasubopt.xml --- a/rnasubopt.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnasubopt.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -93,6 +93,10 @@ <data format="txt" name="output"/> </outputs> <tests> + <test> + <param name="input" value="rnasubopt_input1.fa"/> + <output name="output" file="rnasubopt_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 rnaup.xml --- a/rnaup.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/rnaup.xml Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -80,6 +80,10 @@ <data format="tar" name="accesibilitiesFile"/> </outputs> <tests> + <test> + <param name="input" value="rnaup_input1.fa"/> + <output name="output" file="rnaup_result1.txt"/> + </test> </tests> <help> <![CDATA[ |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rna2dfold_input1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rna2dfold_input1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. +.((((((..(((..........))).(((((.......))))).....(((((.......))))))))))).. |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rna2dfold_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rna2dfold_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90) +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90) <ref 1> +.((((((..(((..........))).(((((.......))))).....(((((.......))))))))))).. (-17.20) <ref 2> +k l en structure |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaaliduplex_input1.clustal --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaaliduplex_input1.clustal Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +CLUSTAL 2.1 multiple sequence alignment + + +Anolis_carolinensis_chrUn_GL34 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +Anolis_carolinensis_chrUn_GL35 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA + ************************************** ************** ******* ********* + |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaaliduplex_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaaliduplex_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(((((((..(.......((((..(..((((((..((((((.......((((((..(..(((((..(((((((.&)))))))..).......))))..)..))))))..)))))).......))))))..)..)))))..))))))). 1,73 : 1,73 (-39.70) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaalifold_input1.clustal --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaalifold_input1.clustal Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +CLUSTAL 2.1 multiple sequence alignment + + +Anolis_carolinensis_chrUn_GL34 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +Anolis_carolinensis_chrUn_GL35 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA + ************************************** ************** ******* ********* + |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaalifold_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaalifold_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUCGAUGCCCACAUUCUCCA +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-25.85 = -25.60 + -0.25) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnacofold_input1.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnacofold_input1.fas Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnacofold_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnacofold_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,3 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +.((((((..((((........)))).(((((.......))))).....(((((((((((.(((((((((((..&.))))))..((((........)))).(((((.......))))).....))))))))))).))))))))))).. (-55.70) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnadistance_input1.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnadistance_input1.fas Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnadistance_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnadistance_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,1 @@ +f: 4 |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaduplex_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaduplex_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaduplex_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaduplex_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,3 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC +.((((((..((......((((...((((..(((.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..))))))..)))..)))).......)))).)))))))). 1,73 : 1,72 (-40.30) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaeval_input1.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaeval_input1.fas Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,3 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaeval_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaeval_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnafold_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_input2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnafold_input2.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_output1.tar |
| b |
| Binary file test-data/rnafold_output1.tar has changed |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnafold_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90) +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-28.70) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnafold_result2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnafold_result2.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +......................(((....)))........(((((...(((((.......))))).))))).. ( -3.39) +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA +(((((((...............(((....)))................(((((.......)))))))))))). ( -4.71) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaheat_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaheat_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +> comment 1 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaheat_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaheat_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,102 @@ +> comment 1 +0 0.0504916 +1 45.2129 +2 -22.6074 +3 -45.4315 +4 -22.7654 +5 45.8852 +6 0.0698557 +7 0.0752356 +8 0.0811424 +9 0.0878275 +10 0.0952985 +11 0.103563 +12 0.11263 +13 0.122506 +14 0.134201 +15 0.147482 +16 0.161608 +17 0.177852 +18 0.196997 +19 0.216779 +20 0.238736 +21 0.264173 +22 0.292607 +23 0.322778 +24 0.357032 +25 0.395149 +26 0.437165 +27 0.482593 +28 0.532254 +29 0.586448 +30 0.645484 +31 0.708343 +32 0.775859 +33 0.84754 +34 0.922752 +35 1.00153 +36 1.08295 +37 1.16636 +38 1.25124 +39 1.3361 +40 1.42079 +41 1.5038 +42 1.58485 +43 1.66306 +44 1.73829 +45 1.80923 +46 1.87712 +47 1.94176 +48 2.00355 +49 2.06245 +50 2.11985 +51 2.1763 +52 2.23277 +53 2.28969 +54 2.34834 +55 2.40888 +56 2.47175 +57 2.53748 +58 2.60638 +59 2.67862 +60 2.75422 +61 2.83314 +62 2.91548 +63 3.00222 +64 3.09214 +65 3.1846 +66 3.28007 +67 3.38221 +68 3.4979 +69 3.61577 +70 3.73136 +71 3.85079 +72 3.98807 +73 4.13409 +74 4.28792 +75 4.45835 +76 4.63996 +77 4.83693 +78 5.05746 +79 5.29359 +80 5.51312 +81 5.69891 +82 5.84747 +83 5.9541 +84 6.02318 +85 6.0546 +86 6.04743 +87 5.99966 +88 5.92173 +89 5.8316 +90 5.7362 +91 5.63003 +92 5.50616 +93 5.36588 +94 5.21371 +95 5.0571 +96 4.90551 +97 4.77223 +98 4.66389 +99 4.57469 +100 4.49084 |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnainverse_input1.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnainverse_input1.fas Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). +gggccccnnaauunnnnnnnnaauunGGGGcnnnnnnnAAAAAnnnnnuuuuannnnnnnuaaaaggggcccn |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnalalifold_input1.clustal --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnalalifold_input1.clustal Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +CLUSTAL 2.1 multiple sequence alignment + + +Anolis_carolinensis_chrUn_GL34 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +Anolis_carolinensis_chrUn_GL35 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA + ************************************** ************** ******* ********* + |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnalalifold_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnalalifold_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +(((.(((((.(((((.......))))).)...(((((.......))))).))))))) (-18.55) 17 - 73 +((((........)))). ( -5.10) 10 - 26 +GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUCGAUGCCCACAUUCUCCA + |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnalfold_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnalfold_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnalfold_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnalfold_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,31 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +.((((....)))). ( -0.20) 56 +.(((..((((....)))).))). ( -3.60) 51 +.(((((.......))))). ( -7.30) 48 +.((((..(((((.......)))))..)))). (-10.80) 42 +.(((((...(((((.......))))).))))). (-11.70) 40 +.((.(((((...(((((.......))))).))))))) (-12.10) 37 +.((((.......)))). ( -2.60) 27 +.(.(((((.......))))).). ( -6.20) 24 +.((((....)))). ( -2.50) 21 +.((.((((....)))).)). ( -4.90) 18 +.(((.(((.(.((((....))))).))).))). ( -7.30) 11 +.((((........)))). ( -5.20) 9 +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))). (-21.90) 1 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA + (-21.90) +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +.((((....)))). ( -0.30) 56 +.(((..((((....)))).))). ( -3.60) 51 +.(((((.......))))). ( -8.80) 48 +.((((..(((((.......)))))..)))). (-12.30) 42 +.(((((...(((((.......))))).))))). (-12.90) 40 +.((.(((((...(((((.......))))).))))))) (-13.60) 37 +.((((.......)))). ( -4.50) 27 +.(.(((((.......))))).). ( -8.10) 24 +.((((.(((((.......))))).)...(((((.......)))))...))). (-17.70) 21 +.(((.(((((.(((((.......))))).)...(((((.......))))).))))))) (-19.50) 16 +.((((........)))). ( -5.20) 9 +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-28.70) 1 +GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA + (-28.70) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapaln_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnapaln_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapaln_input1.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnapaln_input1.fas Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,1 @@ +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapaln_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnapaln_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,7 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +68.8704 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +,((((((..((((........)))).(((((.......))))).....(((((.......)))))))))})}, +GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapdist_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnapdist_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapdist_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnapdist_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,3 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +8.71852 |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapkplex_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnapkplex_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnapkplex_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnapkplex_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -0,0 +1,6 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +.((((((..((((........)))).(((((.......))))).[[[.(((((]]]....))))))))))).. (-31.38) +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA +(((((((..((((..[[[.[[)))).(((((.]].]]]))))).....(((((.......)))))))))))). (-37.04) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplex_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaplex_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplex_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaplex_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..)))))) 34,73 : 1,40 (-24.40) + |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplfold_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaplfold_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplfold_result1.txt |
| b |
| Binary file test-data/rnaplfold_result1.txt has changed |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplot_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaplot_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaplot_input1.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaplot_input1.fas Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,3 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90) |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasnoop_input1a.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnasnoop_input1a.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>homo +CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAAAAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGAAUCCCCGCCCCGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGCCGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCGGUAGCGGCCGGCGCGCGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCAGCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAACAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAACCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGCGGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCCCCCCGUUCCUCCCGACCCCUCCACCCGCCCUCCCUUCCCCCGCCGCCCCUCCUCCUCCUCCCCGGAGGGGGCGGGCUCCGGCGGGUGCGGGGGUGGGCGGGCGGGGCCGGGGGUGGGGUCGGCGGGGGACCGUCCCCCGACCGGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGGACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGGGGGCCCCGUCCGUCCGUCCGUCCUCCUCCUCCCCCGUCUCCGCCCCCCGGCCCCGCGUCCUCCCUCGGGAGGGCGCGCGGGUCGGGGCGGCGGCGGCGGCGGCGGUGGCGGCGGCGGCGGGGGCGGCGGGACCGAAACCCCCCCCGAGUGUUACAGCCCCCCCGGCAGCAGCACUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUCGCCGCGCUCUCCCCCCUCCCGGCGCCCACCCCCGCGGGGAAUCCCCCGCGAGGGGGGUCUCCCCCGCGGGGGCGCGCCGGCGUCUCCUCGUGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUCUCCCACCCCUCCUCCCCGCGCCCCCGCCCCGGCGACGGGGGGGGUGCCGCGCGCGGGUCGGGGGGCGGGGCGGACUGUCCCCAGUGCGCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGAGGUUCUCUCGGGGCCACGCGCGCGUCCCCCGAAGAGGGGGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCCACCCGACCCGUCUUGAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCGCACGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGGAUCCCGAGGCCUCUCCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCACGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGUCGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAGGAUAGCUGGCGCUCUCGCAGACCCGACGCACCCCCGCCACGCAGUUUUAUCCGGUAAAGCGAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGUAAGAAGCCCGGCUCGCUGGCGUGGAGCCGGGCGUGGAAUGCGAGUGCCUAGUGGGCCACUUUUGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGCCGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGACGGGAGCGGCGGGGGCGGCGCGCGCGCGCGCGCGUGUGGUGUGCGUCGGAGGGCGGCGGCGGCGGCGGCGGCGGGGGUGUGGGGUCCUUCCCCCGCCCCCCCCCCCACGCCUCCUCCCCUCCUCCCGCCCACGCCCCGCUCCCCGCCCCCGGAGCCCCGCGGACGCUACGCCGCGACGAGUAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGCAGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGGAGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGAGCGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGAGUCGGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGUAACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUGAAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCGUCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGGUGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUCUGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGCUGGGUCGGUCGGGCUGGGGCGCGAAGCGGGGCUGGGCGCGCGCCGCGGCUGGACGAGGCGCGCGCCCCCCCCACGCCCGGGGCACCCCCCUCGCGGCCCUCCCCCGCCCCACCCGCGCGCGCCGCUCGCUCCCUCCCCACCCCGCGCCCUCUCUCUCUCUCUCUCCCCCGCUCCCCGUCCUCCCCCCUCCCCGGGGGAGCGCCGCGUGGGGGCGCGGCGGGGGGAGAAGGGUCGGGGCGGCAGGGGCCGCGCGGCGGCCGCCGGGGCGGCCGGCGGGGGCAGGUCCCCGCGAGGGGGGCCCCGGGGACCCGGGGGGCCGGCGGCGGCGCGGACUCUGGACGCGAGCCGGGCCCUUCCCGUGGAUCGCCCCAGCUGCGGCGGGCGUCGCGGCCGCCCCCGGGGAGCCCGGCGGCGGCGCGGCGCGCCCCCCACCCCCACCCCACGUCUCGGUCGCGCGCGCGUCCGCUGGGGGCGGGAGCGGUCGGGCGGCGGCGGUCGGCGGGCGGCGGGGCGGGGCGGUUCGUCCCCCCGCCCUACCCCCCCGGCCCCGUCCGCCCCCCGUUCCCCCCUCCUCCUCGGCGCGCGGCGGCGGCGGCGGCAGGCGGCGGAGGGGCCGCGGGCCGGUCCCCCCCGCCGGGUCCGCCCCCGGGGCCGCGGUUCCGCGCGCGCCUCGCCUCGGCCGGCGCCUAGCAGCCGACUUAGAACUGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCGCGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGUCCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGAGAGGUGUAGAAUAAGUGGGAGGCCCCCGGCGCCCCCCCGGUGUCCCCGCGAGGGGCCCGGGGCGGGGUCCGCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGCCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCGGUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCGCCAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUUCAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGAACGAUACGGCAGCGCCGCGGAGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCUGUCCCCGCCGGCGGGCCGCCCCCCCCUCCACGCGCCCCGCCGCGGGAGGGCGCGUGCCCCGCCGCGCGCCGGGACCGGGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGGCCGGAAAGGCGGCCGCCCCCUCGCCCGUCACGCACCGCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGUUUCGUACGUAGCAGAGCAGCUCCCUCGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUUUGUC |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasnoop_input1b.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnasnoop_input1b.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>ACA51 +AACCTACCCCATATACACCTCAGCTCAGGCCCTGTGCCTGGTCTGTATTGTGAATGGGGGAACATAG |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasnoop_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnasnoop_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>ACA51 +>homo +<<<<<<.|.<<<.<<<&(.>>>.>>>.((.((((...............................)))).))>>>>>>...).. 807,822;814 : 4,62 (-33.20 = -13.20 + -11.90 + -11.60 + -0.60 + 4.1 ) (-23.60) +UCCUCCCUCGGGAGGG&AACCUACCCCAUAUACACCUCAGCUCAGGCCCUGUGCCUGGUCUGUAUUGUGAAUGGGGGAACAUAG |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasubopt_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnasubopt_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnasubopt_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnasubopt_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| [ |
| @@ -0,0 +1,10 @@ +> Anolis_carolinensis_chrUn_GL343590.trna2-A [100] +UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA -2190 100 +(((((((..((((........)))).(((((.......))))).....(((((.......))))))))).))) -21.70 +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). -21.20 +.(((((...((((........)))).(((((.......))))).....(((((.......))))).))))).. -20.90 +.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. -21.90 +> Anolis_carolinensis_chrUn_GL343207.trna3-A [100] +GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA -2870 100 +((((((...((((........)))).(((((.......))))).....(((((.......))))).)))))). -27.70 +(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). -28.70 |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaup_input1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaup_input1.fa Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55 +TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15 +GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 test-data/rnaup_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnaup_result1.txt Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -0,0 +1,6 @@ +>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC + 55, 58 (0.021) for u= 4 +RNAup output in file: Anolis_carolinensis_chrUn_GL343590.trna2-A_u1.out +>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC + 16, 19 (0.003) for u= 4 +RNAup output in file: Anolis_carolinensis_chrUn_GL343207.trna3-A_u1.out |
| b |
| diff -r ec0fdb8c4ebb -r 5e58cbf27a05 tool_dependencies.xml --- a/tool_dependencies.xml Wed Feb 04 12:45:16 2015 -0500 +++ b/tool_dependencies.xml Mon Feb 09 13:26:11 2015 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="vienna_rna" version="2.1"> - <repository changeset_revision="276d1f7a4d05" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3b53eda26527" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |