' + + '' + + _("Hide Search Matches") + + "
" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/docs/genindex.html b/docs/genindex.html new file mode 100644 index 0000000..1c0900b --- /dev/null +++ b/docs/genindex.html @@ -0,0 +1,104 @@ + + + + + ++++
+- +
HogProf is an extensible and tunable approach to phylogenetic profiling using orthology data. It is powered by minhash based datastructures and computationally efficient.
- +
Still under major development and may change.
To install My Project, run the following command:
+Using pip
+Or from github +.. code-block:: bash +$ git clone https://github.com/DessimozLab/HogProf.git +$ pip install -r pipreqs.txt .
+To use the library we need an OMA instance’s HDF5 file containing HOG info and some accesory files.
+Let’s create a directory for the phylogenetic rpfiling database were going to make.
+Ok. We’re ready! Now let’s compile a database containing all HOGs and our desired taxonomic levels using default settings. Launch the lshbuilder. +dbtypes available on the command line are : all , plants , archaea, bacteria , eukarya , protists , fungi , metazoa and vertebrates. These will use the NCBI taxonomy as a tree to annotate events in different gene family’s histories.
+This should build a taxonomic tree for the genomes contained in the release and then calculate enhanced phylogenies for all HOGs in OMA. +Once the database is completed it can be interogated using a profiler object. Construction and usage of this object should be done using a python script or notebook.
+If you encounter any issues while using My Project, please file a bug report on our GitHub repository: https://github.com/user/repo/issues
+My Project was created by John Doe.
+