Mercurial > repos > bgruening > dotknot

diff test-data/test2_output.txt @ 0:42d20ff5da1b draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
author bgruening
date Thu, 17 Sep 2015 17:10:07 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2_output.txt	Thu Sep 17 17:10:07 2015 -0400
@@ -0,0 +1,56 @@
+Include kissing hairpins.
+Show best local pseudoknots.
+Show predicted global structure.
+
+> PKB171 human coronavirus 229E, coronavirus; ribosomal frameshifting; polymerase
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+Sequence length:  54
+Using PKB171 as file identifier
+
+DotKnot is running...
+Predicting pseudoknots...
+Predicting kissing hairpins...
+
+Detected pseudoknots and kissing hairpins:
+1 54 -41.2
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
+
+
+Best 5 pseudoknots and kissing hairpins in terms of energy to length ratio:
+1 54 -41.2
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
+1 46 -26.23
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGC
+((((((((((((...[[[[[)))))))))))).........]]]]]
+11 54 -18.12
+GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+(((..((((.....))))....[[[[[[[))).....]]]]]]]
+16 37 -7.79
+GCUCGACUAGAGCCCUGUAUGG
+((((..[[[))))......]]]
+11 48 -13.12
+GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAG
+(((..((((.....)))).[[[[......)))..]]]]
+
+Best 5 pseudoknots and kissing hairpins in terms of free energy:
+1 54 -41.2
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))
+1 46 -26.23
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGC
+((((((((((((...[[[[[)))))))))))).........]]]]]
+11 54 -18.12
+GUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+(((..((((.....))))....[[[[[[[))).....]]]]]]]
+3 54 -16.6
+GGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+(((......[[[.((((.....))))))).(((((((.....]]])))))))
+2 54 -16.2
+GGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+(((...........[[[[[.......)))..(((((((..]]]]].)))))))
+
+Predicted global structure
+CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUGGACCACGAGCAGUCCAUG
+((((((((((((...[[[[[))))))))))))(((((((..]]]]].)))))))