explore_database.py

Examine the composition of the database using taxonomic terms as search queries.

explore_database.py [OPTIONS]

Optional arguments:

  • -d, --database <db_dir> Path to the database directory if config.py has not been run.
  • -t, --higher_taxonomy Show higher taxonomy and number of taxa in each group in the database.
  • -l, --lower_taxonomy Show lower taxonomy and number of taxa in each group in the database.
  • -r, --get_higher <HigherTax> Return table with all taxa assigned the given higher taxonomy that displays the UniqueID, Long Name, Higher and Lower taxonomy, the number of orthologs, and the number of paralogs present in the database.
  • -w, --get_lower <LowerTax> Return table with all taxa assigned the given lower taxonomy that displays the UniqueID, Long Name, Higher and Lower Taxonomy, the number of orthologs, and the number of paralogs present in the database.
  • -o, --get_org <UniqueID> For the given Unique ID returns the Long Name, Higher and Lower Taxonomic Designation, Data Type, Orthologs (number present in the database for the taxon), Paralogs (number present in the database for the taxon), and the Accession.