2.3. Inserting a new organism

2.3.1. Insert organism

Every data file you’ll load (eg. fasta, gff, blast) must belong to an organism. These are instructions to insert a new organism to the database if you did NOT load the NCBI taxonomy or if the organism you’re working with is not included.

python manage.py insert_organism --genus 'Organismus' --species 'ineditus'
  • There are optional fields you can provide. Please take a look at the command help (–help).

2.3.2. Remove organism

If, by any reason, you need to remove an organism you should use the command remove_organism. Most data files you’ll load depend on the organism record (eg. fasta, gff, blast). If you delete an organism, every data file you loaded that depend on it will be deleted on cascade.

python manage.py remove_organism --help
  • These commands require the following info: Organism.genus and Organism.species