The edit command is used to edit objects (e.g., map set tree nodes and track trees) added to the Persephone database. The edit command will open a menu-driven editor letting you edit configurable items. The syntax is as follows:

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

where "id" is the ID number of the map set track tree node or track tree and "path" is the path name of the map set track tree node or track tree (e.g., "/Arabidopsis thaliana/ARATH_TAIR_chr_V10").

The table below lists the definitions for the edit 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 edit, which can be mapsettreenode or tracktree.

id

or
path

Required

  • id. The ID number of the object you want to edit.
  • path. The path name of the object you want to edit (e.g., "/Arabidopsis thaliana/ARATH_TAIR_chr_V10".) Please note you must use double quote marks (") if the path contains any spaces.

-v

Optional

Executes the edit command in verbose mode.

-t

Optional

Executes the edit command in test mode.

-d

Optional

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

-f

Optional

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

Editing a Map Set Tree Node

To edit a map set tree node, enter edit followed by mapsettreenode and the ID number or path name of the node. The following shows an example of editing a node with an ID number of 269260457.

PS> edit mapsettreenode 269260457
MapSetId?
DisplayName? test3
ParentId? 269260456
OrderNo? 1

If you make any changes, a confirmation message similar to the following will be displayed.

1 MapSetTreeNode(s) has been successfully modified.

Editing a Track Tree

To edit a map set track tree, enter edit followed by tracktree and the ID number or path name of the track tree. The following shows an example of renaming a track tree node given a map set path:

PS> edit tracktreenode "Arabidopsis thaliana/Arabidopsis annotation v. 10"
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] Blast Tracks (Group, Order: 16)
 [7] PLANT_NR_HITS (Track, Order: 12, Type: Alignment)
 [8] blast vs plant_nr (Track, Order: 14, Type: Alignment)
 [9] plant nr tblastn (Track, Order: 15, Type: Alignment)
 [10] plant_nr partitioned (Track, Order: 16, Type: Alignment)
 [11] plant nr partitioned 3 (Track, Order: 17, Type: Alignment)
[12] Bedgraph Tracks (Group, Order: 17)
 [13] Large Bedgraph Tracks (Group, Order: 17)
  -- no items --
Enter [NodeNumber] to edit? 7
NodeName? PLANT_NR
Parent [NodeNumber]? 6
OrderNo? 12
IsShownFirst? False
Do you really want to UPDATE the TrackTreeNode? (Y/N) Y
Success.

Here, the flag IsShownFirst specifies whether a track should be shown when a map is opened for the first time.

Similar commands can change the order of nodes in the tree or move the whole branches by changing parent nodes.