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Tree exports - nexus - add lists within the comments blocks #503

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4 tasks done
GoogleCodeExporter opened this issue Mar 27, 2015 · 4 comments
Closed
4 tasks done

Tree exports - nexus - add lists within the comments blocks #503

GoogleCodeExporter opened this issue Mar 27, 2015 · 4 comments
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@shawnlaffan
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auto-migrated enhancement
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Release_2.0

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GoogleCodeExporter commented Mar 27, 2015 •
edited by shawnlaffan
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It would be useful to put list results within comments blocks within the
trees. These can be done as key=value pairs.

These can then be plotted/analysed etc using software which supports their use.

Original issue reported on code.google.com by shawnlaffan on 11 Sep 2014 at 6:44

To do:

  • add option to nexus export
  • update format to match spec
  • ensure we don't leave lists behind (clean up the comment block data as needed)
  • ensure colours are exported with lists if requested
@shawnlaffan shawnlaffan self-assigned this Apr 9, 2015
@shawnlaffan shawnlaffan added this to the Release_2.0 milestone Nov 8, 2016
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See FigTree example data for a template.

@shawnlaffan shawnlaffan mentioned this issue Dec 2, 2016
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@LukedFitzpatrick LukedFitzpatrick mentioned this issue Jan 23, 2017
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shawnlaffan commented Feb 17, 2017 •
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http://treegraph.bioinfweb.info/Help/wiki/Open_files#Nexus_format_with_additional_annotations
https://code.google.com/archive/p/beast-mcmc/wikis/NexusMetacommentFormat.wiki

@shawnlaffan shawnlaffan mentioned this issue Feb 21, 2017
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@shawnlaffan shawnlaffan changed the title Tree exports - nexus and newick - add lists within the bootstrap block Tree exports - nexus and newick - add lists within the comments blocks Feb 21, 2017
@shawnlaffan shawnlaffan changed the title Tree exports - nexus and newick - add lists within the comments blocks Tree exports - nexus - add lists within the comments blocks Feb 21, 2017
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shawnlaffan commented Feb 21, 2017 •
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Most of the changes to implement this were done under the branch for issue #630

shawnlaffan added a commit that referenced this issue Aug 22, 2017
@shawnlaffan
Add option to export tree lists to nexus format files
8728cde 
Tests need to be updated since the format of the lists
has changed to work with FigTree (which presumably follows
the spec).

Updates #503
shawnlaffan added a commit that referenced this issue Aug 22, 2017
@shawnlaffan
Update test expectation given format has changed
1c6a200 
Updates #503
shawnlaffan added a commit that referenced this issue Aug 22, 2017
@shawnlaffan
Avoid an undef warning
8942353 
Updates #503
shawnlaffan added a commit that referenced this issue Aug 22, 2017
@shawnlaffan
Rename the bootstrap test file so it is adjacent to the tree test file
7fa5b0f 
Updates #503
shawnlaffan added a commit that referenced this issue Aug 22, 2017
@shawnlaffan
Simplify the comments block cleanup
b82e662 
Updates #503
shawnlaffan added a commit that referenced this issue Aug 22, 2017
@shawnlaffan
Comment out some code
33dc86c 
This is handled inside the called sub

Updates #503
shawnlaffan added a commit that referenced this issue Aug 22, 2017
@shawnlaffan
Add tests for nexus list and colour exports
6a984f6 
Updates #503
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Mark as fixed

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