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files and syntax for extract_clade_placements

Hi Lucas,

Thank you for producing genesis.  I've successfully compiled it and the two demo apps, and I can run visualize_placements successfully

./visualize_placements test_a.jplace test_a.nexus

Would you please make available some test files for extract_clade_placements?  Specifically, I'd like to see a file for the second argument ("A directory path, which needs to contain a single file for each clade of the reference tree.")  

We are running epa and pplacer against a reference tree for mammals (16S), and so creating this clade names file will take some effort, and i'd like to see an example.  

Thank you in advance, and thank you again for genesis.

Doug




Comments

  • edited April 2016
    Hi Doug,

    thanks for your feedback, and sorry for the late answer, I was sick the last couple of days.

    I just released a new version of genesis (https://github.com/lczech/genesis/releases/tag/v0.5.0), which contains, example files for the demo. You find instructions in the manual (http://doc.genesis-lib.org/demos_extract_clade_placements.html).

    As for creating the clade files with lists of taxa names for each clade, have a look at Dendroscope (http://dendroscope.org/). You can load a tree file (newick, nexus and some other formats), then select a subtree/clade (using either the mouse or some of the options in the "Select" menu, and then simply use copy (ctrl+c) to copy all selected node names. You can then paste them to some text file (ctrl+v), replace the tab characters by new line characters, and save it to a file, which can then be used for the demo.

    Hope that helps. Let me know if you have any more questions.
    Lucas
  • Remark: Extracting the clades from a tree is a bit cumbersome to do manually, I know. Unfortunately, it is inherently a manual task, as it is your choice which subtrees you want to group into a clade. Tree visualization tools (like Dendroscope) can help, but ultimately, the biological relationships you want to express in a clade are case-dependent.

    However, if you know of any tools that help to select extract clades from a given tree and store them in some file format, please let me know. I am not aware of any, but it would make life easier if genesis could read such files.
  • Thanks very much for the update and the new files.  I tried make update to compile the demo apps and got compiler errors (and no compiled apps).  I will, however, try to work with the 0.4.0 code using the demo files.  

    I can't paste all the errors, but here is some:

    /gpfs/home/b042/scripts/genesis-0.5.0/apps/visualize_placements.cpp: In function ‘void write_color_tree_to_nexus(const PlacementTree&, const std::vector<genesis::utils::Color>&, const string&)’:

    /gpfs/home/b042/scripts/genesis-0.5.0/apps/visualize_placements.cpp:163:17: error: ‘make_unique’ was not declared in this scope

         auto taxa = make_unique<utils::NexusTaxa>();

                     ^


    ...

    /gpfs/home/b042/scripts/genesis-0.5.0/lib/utils/core/std.hpp:66:20: note:   ‘genesis::utils::make_unique’ std::unique_ptr<T> make_unique(Args&&... args)                    ^/gpfs/home/b042/scripts/genesis-0.5.0/apps/visualize_placements.cpp:163:45: error: expected primary-expression before ‘>’ token     auto taxa = make_unique<utils::NexusTaxa>();                                             ^/gpfs/home/b042/scripts/genesis-0.5.0/apps/visualize_placements.cpp:163:47: error: expected primary-expression before ‘)’ token     auto taxa = make_unique<utils::NexusTaxa>();                                               ^/gpfs/home/b042/scripts/genesis-0.5.0/apps/visualize_placements.cpp:168:47: error: expected primary-expression before ‘>’ token     auto trees = make_unique<utils::NexusTrees>();                                               ^/gpfs/home/b042/scripts/genesis-0.5.0/apps/visualize_placements.cpp:168:49: error: expected primary-expression before ‘)’ token     auto trees = make_unique<utils::NexusTrees>();













                                                     ^
  • Thanks also for the dendroscope tip. 
  • edited April 2016
    Fixed it, see genesis v0.5.1: https://github.com/lczech/genesis/releases/tag/v0.5.1

    Note to myself: test all demo files before releasing a new version ;-)
  • edited April 2016
    Note to the note: added automated testing of the demo programs before releasing a new version. ;-)
    Goodbye compilation errors.
  • edited June 2016
    Hi Doug and Charles,

    I just released genesis v0.8.0 (https://github.com/lczech/genesis/releases/tag/v0.8.0), where instead of this complicated clade format with different files in a directory, we now use a single file with tab separated lines for each taxon.

    See here for the updated documentation of the demo: http://doc.genesis-lib.org/demos_extract_clade_placements.html

    This might be more convenient for you to use. If you decide to try it out, let me know in case there are any issues.

    All the best
    Lucas
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