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_reactome populate. By default this command populates the database only with human information. In order to populate all species pathway information you can add the “–not-only-human” argument. 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_reactome drop. More logging can be activated by added “-vv” or “-v” as an argument.

• Export gene sets as an excel file: python3 -m bio2bel_reactome export. By default, the excel will contain all pathways from all species. However, you can add the argument “species” and type the name of a particular one to get only those pathways (e.g., “–species=’Homo sapiens’””). Since Reactome has a hierarchy pathway structure, you can get only the major pathways with the optional parameter “–top-hierarchy”.