Description from GitHub readme.md:

PanelApp tools

This containts a simple class to interact with the PanelApp API. See the (PanelApp website)[https://panelapp.genomicsengland.co.uk/]

The main class is PanelApp.

This also expose a cli command panelapp_dump that can be used to download PanelApp panels to tables. By default, it will download GREEN and AMBER genes for all panels in GRCh38 version into panelapp_[currentdate] folder.

You can user arguments to change genome build, output folder and gene confidence level (see --help)

Following methods are available in the PanelApp class

• listPanels(self, panel_id=False, name=False, disease=False) : Return pandas dataframe of panels based on the search criteria. When no criteria used returns for all panels. Search criteria work as OR.

• getPanelId(self, name='.*', disease='.*') Return list of panels ids according to the search criteria. Search criteria work as OR.

• getGenes(self, pid=False, name=False, disease=False, level=3, out_format="df", build="GRCh38") Return True/False (indicating if any genes found) and a pandas dataframe for the genes of interest. First search for relevant panels using the pid, name and disease, then for the resulting panels get genes informations for genes with level above the value set by level option (level 3 = GREEN genes, 2 = AMBER, 1 = RED). You can ask for GRCh38 or GRCh37 coordinates and the returned dataframe can be structure as a BED file using out_format="bed"

• dumpPanels(self, output_dir, panels="all", level=3, build="GRCh38") Save panels to disk as tables of genes named by panel id and also save a index table describing panels for each panel id. You can pass a list of panel ids to panels or use all to save all panels. You can set the minimum level of confidence for saved genes using level and the genome build for coordinates using build.