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[Treebase-guts] [ treebase-Bugs-3303390 ] Some tree newicks do not end in semi-colons
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From: SourceForge.net <no...@so...> - 2011-06-29 15:42:07
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Bugs item #3303390, was opened at 2011-05-17 11:40 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303390&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Some tree newicks do not end in semi-colons Initial Comment: It appears that when TreeBASE downloads trees, the newick string is pulled straight from the "newickstring" field in the phylotree table, instead of being reconstructed on the fly using the nodes and edges. Some of these trees are missing a semi-colon at the end of the newickstring. For example, in study S10830, tree Tr25629 is missing a semi-colon, while tree Tr25630 is not missing the semi-colon. The missing semi-colon can happen as a result of rerooting the tree using PhyloWidget and then saving the new rerooted tree back to the "newickstring" field. But however this creeps in, whenever trees are written, we should check to add a semi-colon to the end of the newick string. For example, all these links end up creating trees in newick, and in each case they are missing the semi-colon for Tr25629: http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr25629?format=nexus http://www.treebase.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=6642&id=10830 http://www.treebase.org/treebase-web/search/downloadATree.html?id=10830&treeid=25629 http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr25629 http://purl.org/phylo/treebase/phylows/study/TB2:S10830?format=nexus ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303390&group_id=248804 |
