When you add data to your Persephone database, PersephoneShell tags this addition as a run with a unique ID, known as a RunId. You can use the List command to list runs and their RunIds along with what sort of object (e.g., an annotation) was added and when it was added to your Persephone database.

In addition, once you have identified the RunId and what was added during that run, you can use the RunId along with the Delete command to delete the object from your Persephone database. The steps required to delete an object are described below.

Note

This section is a "use case" for this example indented to provide quick steps to delete objects in your Persephone database with the List and Delete commands. For complete syntax of these commands please refer to List and Delete for more information.

Note that there are multiple ways of deleting the objects in the database: mapset, tracktreenode, variants, etc. Some of the objects (like otholog pairs) can be deleted only by using their RunId assigned during loading.

Step 1: Identify the RunID

Before you can delete an object, you need to identify the run where it was added and the corresponding RunId using the List command. For example, enter the following to list the top 5 runs in "long-listing" format in reverse chronological order

PS> list runs -l -r -t 1

The following is a typical example of the output.

RUN_ID    DESCRIPTION    PROCESS_TYPE    DATE_CREATED    CREATED_BY    PARENT_RUN_ID
------------------------------------------------------------------------------------
200     Add true genetic maps for wheat from https://doi.org/10.1371/journal.pone.0186329.s003.zip  LOAD MAPS   7/27/2018 11:53:19 PM   operator    (null)
1 run

In the example above, there is  the most recent run with the RunId=200 that loaded markers.

To narrow down the search, when looking for a run of particular type (e.g., orthologs), specify the type of the batch job using "-T <job type>", e.g.

list run -l -T ortholog

This "job type" is the term used after the add verb when loading the data (add annotation, add ortholog, add qtls, etc).

Step 2: Delete the Object

Once you have identified the RunID of the run that added the object or objects you want to delete, use the Delete command to delete the run and the object or objects it added. For example, enter the following to test deleting the run with the RunId of "200" that had added markers:

PS> delete run 200 -t

The following confirmation message will be displayed.

This operation will affect:
  - 35768 annotations
  - 13 tracks
run 200 can be removed

In the verbose mode, before deleting the objects associated with the given run, the program will ask for a confirmation. The confirmation can be avoided by using the switch '-f' (force).