Phylesystem is a series of git repository used to store phylogenetic statements (typically published trees). You can download the full set of phylesystem shards (there is only one, at this point) by following the instructions on https://github.com/OpenTreeOfLife/phylesystem and then pointing peyotl to your local copy of phylesystem as described on the Configuration page.
If you have a local copy of the phylesystem, then you can peyotl’s PhylesystemAPIWrapper to use your local copy by using
get_from='local' when creating an instance of the wrapper:
from peyotl.api.phylesystem_api import PhylesystemAPI phylesystem_api_wrapper = PhylesystemAPI(get_from='local') local_phylesystem_controller = phylesystem_api_wrapper.phylesystem_obj for study_id, file_path in local_phylesystem_controller.iter_study_filepaths(): print study_id, 'is in', file_path
You can perform the phylesystem_api functions on a local version of the PhylesystemAPI class, as well.
But the wrappers created using
get_from='local' are the only ones that allow you to iterate over all studies.
scripts/phylesystem/ot_phylesystem_list_tags.py script demonstrates iterating
over every study in a local version of the repository and printing the study and
phylesystem section of the configuration file has settings that control
the size of files allowed in the phylesystem.