Command Line Interface

The command line interface allows you to communicate with the package and perform basic functions such as:

  • Populate the database: python3 -m bio2bel_kegg populate. By default the database is reset every time is populated. However, another optional parameter “–reset-db=False”, allows you to avoid the reset. More logging can be activated by added “-vv” or “-v” as an argument.

  • Drop the database: python3 -m bio2bel_kegg drop. More logging can be activated by added “-vv” or “-v” as an rgument.

  • Export gene sets as an excel file: python3 -m bio2bel_kegg export.