The delete command is used to delete objects (e.g., map set tree nodes, organisms, map sets, annotations, markers, alignments, synteny, ontologies, orthologs, variants, and runs) you added from the Persephone database. The syntax is as follows:

delete {target} {id|path} [-v | -d | (-t | -f)]

where "id" is the RunId number that can be identified with the List command (see List for more information) and "path" is the path name of the object (e.g., "/Arabidopsis thaliana/test1/test2/test3").

The table below lists the definitions for the delete command parameters. Please note you must use either the "id" or "path" but not both.

Delete Command Parameters

Parameter

Required or Optional?

Definition

{target}

Required

A target is the object type you want to delete, which can be mapsettreenode, organism, mapset, annotations, mapping, markers, alignments, qtls, quantitative, synteny, ontology, expression, tracks, tracktreenode, variants, orthologs, or run.

id

or
path

Required

  • id. Depending on the target it could be RunId or MapSetId. The RunID is the ID of the run that added the object you want to delete. Use the List command to identify the RunId number. (See List for more information.)
  • path. The path name of the object you want to delete (e.g., "/Arabidopsis thaliana/test1/test2/test3") Please note you must use double quote marks (") if the path contains any spaces.

-v

Optional

Executes the delete command in verbose mode.

-t

Optional

Executes the delete command in test mode.

-d

Optional

Executes the delete command in debug mode. You can send the debug output to Persephone Software, LLC. at http://persephonesoft.com/contact.

-f

Optional

Executes the delete command in "force" mode, which bypasses the confirmation prompt in interactive mode.

It is good practice to test (-t) the delete operation before execution. The test will print the list of objects to be deleted:

PS> delete run 35 -t
This operation will affect:
  - 12869 mappings
  - 10 tracks
  - 12869 markers

run 35 can be removed.

Deleting a Target with a RunId

To delete a target with a RunId enter 'delete run' followed by  the RunId number. For example, to delete markers that were added in RunId 35 you would enter the following:

PS> delete run 35 -v

The following message will be displayed.

PS> delete run 35 -v
This operation will affect:
  - 12869 mappings
  - 10 tracks
  - 12869 markers

Do you really want to delete the markers? (Y/N)

 Confirm the deletion if the numbers of the objects to be deleted match your expectations.

Tip

As described above, you use the List command to determine the RunId number. See Deleting Loaded Data for an example of using the List and Delete commands together.

Deleting a Target with a Path

To delete a target with a path, enter delete followed by the target type and the path name. For example, to delete a map set tree node with a path name of "/Arabidopsis thaliana/test1/test2/test3" you would enter the following:

PS> delete mapsettreenode "/Arabidopsis thaliana/test1/test2/test3"

The following message will be displayed.

Mapsettreenodes: "/Arabidopsis thaliana/test1/test2/test3" have been successfully deleted.

 

Note

You must enter the entire path name for a target to be deleted - a map set or a track tree node (wildcards are not supported). Remember that you can use auto-completion using Tab key.

Deleting Track Tree Nodes

Use the delete command followed by the "tracktreenode" keyword and the MapSetId to delete a track tree node. The following shows an example of deleting a track tree node called "FGENESH2 (CDS)" in a map set:

PS> delete tracktreenode "Arabidopsis thaliana/Arabidopsis annotation v. 10" -v
TrackTree for MapSet 'Arabidopsis annotation v. 10':
[0] GENBANK (CDS) (Track, Order: 0, Type: Annotation)
[1] MRNA (Track, Order: 1, Type: Annotation)
[2] Other gene models (Group, Order: 3)
 [3] FGENESH (CDS) (Track, Order: 2, Type: Annotation)
 [4] GlimmerHMM (CDS) (Track, Order: 4, Type: Annotation)
 [5] FGENESH2 (CDS) (Track, Order: 20, Type: Annotation)
[6] Bedgraph Tracks (Group, Order: 15)
 [7] Large Bedgraph Tracks (Group, Order: 17)
  -- no items --
Enter [NodeNumber] to delete? 5
Do you really want to DELETE the TrackNode 'FGENESH2 (CDS)'? (Y/N) Y
This operation will affect:
- 0 annotations
- 5 tracks
Do you really want to delete the tracks? (Y/N) Y
> Deleting 5 tracks...
5 tracks have been removed.

A track tree node name can be a part of the object's path. For example, if a map set "TAIR10" has a track "gene models", the full path on the command line would be "/Arabidopsis thaliana/TAIR10/gene models". The auto-completion will help you assembling the path that includes the track names.