/opentree_pytoys

simple tools to play with opentree resources

Primary LanguagePython

OpenTree PY Toys

Pruning OpenTree synth tree

If you are trying to calculate things on a subset of the OpenTree synth tree, here are some steps to get that done. These require some of the phyx tools and python scripts that are presented here but that should be it. The get_ottids_for_taxa.py script needs the request python module that can be found here.

  • get the latest synth tree from here

  • get OTT ids for your taxa using either

    • the scripts in this repo python get_ottids_for_taxa.py file.ids > file.ids.ottids. The file.ids file should have a Genus species on each line.
    • the peyotl set of tools
    • the OpenTree APIs

  • if you aren't using pxtrt (from phyx)to trace your tree, I recommend pruning it down to just what you use (so, plants for example). You don't have to do this if you use the phyx program pxtrt to trace the tree because it can read larger trees.

    • pxmrcacut -m cut_mrca_plants -t opentree9.1_tree/labelled_supertree/labelled_supertree.tre > vas_opentree_9.1.tre
    • there are included cut_mrca files for different groups in this resources dir in the repo repo
    • pxmrcacut is a program in the phyx package

  • get the list of taxa as a tree

    • using python - python trace_tree.py vas_opentree_9.1.tre file.ids.ottids > vas_nms.tre
    • or you can use pxtrt from phyx. You will need to isolate the ids from file.ids.ottids. You can do this with awk -F '\t' '{print "ott"$2}' file.ids.ottids > file.justids.ottids. Then you can run pxtrt like pxtrt -t opentree9.1_tree/labelled_supertree/labelled_supertree.tre -f file.justids.ottids > traced.tre.

An example with Fire_Border_Hot_Sauce from TacoBell

In the examples folder, there is a TACO_BELL directory. There is a file called border_hot_sauce with the scientific names of the ingredients. Here are the steps to a readable tree:

  • python ../../src/get_ottids_for_taxa.py border_hot_sauce > names_ottids
  • awk -F '\t' '{print "ott"$2}' names_ottids > justids.ottids
  • I have already downloaded the most recent synth (see above) into a directory called opentree9.1_tree. So I run pxtrt opentree9.1_tree/labelled_supertree/labelled_supertree.tre -f justids.ottids > out.tre
  • out.tre is the tree that you want but the ids are ottids, so not really readable. To convert, we do three simple steps:
    • python get_all_names_tre.py out.tre > alltreenames
    • python get_name_for_ottids.py alltreenames > allnames.ottids_names
    • python convert_ottids_names_tre.py out.tre allnames.ottids_names > final.tre

A lot of steps right now but I will simplify soon! Right now, going for flexibility.