To verify that you have successfully performed an operation in PersephoneShell you can use the list command. (See List for more information.) The sections below describe how to use the list command to verify the addition of maps, map sets, and map set trees, respectively.

Verify the Addition of Maps

To very that you have successfully added maps, use the command list maps. As an option, you can use list command parameters to filter your results. For example, entering the following in interactive mode will list the top 10 items in "long-listing format" in reverse chronological order.

list maps -l -r -t 10

To list maps of one map set, specify the map set by its MapSetId or its path. The auto-complete feature (press TAB) will help you typing the map set path. Start typing the first letters (case sensitive!) of the corresponding root node and press TAB, type a forward slash, the TAB again, etc. Pressing TAB repeatedly will list the map sets or other map set tree nodes that match the printed text.

PS> list maps "Glycine max/Wm82.a4.v1" -l -t 10
MAP_ID  MAP_NAME           ACCESSION          LENGTH    CHROM_NAME
--------------------------------------------------------------------
8831    Gm01               Gm01               57932355  01
8832    Gm01_scaffold_166  Gm01_scaffold_166  45523     (null)
8833    Gm02               Gm02               50400358  02
8834    Gm02_scaffold_122  Gm02_scaffold_122  60768     (null)
8835    Gm03               Gm03               46951866  03
8836    Gm03_scaffold_135  Gm03_scaffold_135  54556     (null)
8837    Gm03_scaffold_238  Gm03_scaffold_238  24147     (null)
8838    Gm03_scaffold_245  Gm03_scaffold_245  23189     (null)
8839    Gm03_scaffold_27   Gm03_scaffold_27   329435    (null)
8840    Gm03_scaffold_521  Gm03_scaffold_521  10953     (null)

Verify the Addition of Map Sets

To very that you have successfully added map sets, enter list followed by mapsets. As an option, you can use list command parameters to filter your results. For example, entering the following in interactive mode will list the top item (-t 1) in "long-listing format" (-l) in reverse chronological order (-r).

PS> list mapset -p Wm* -l
MAP_SET_ID  DISPLAY_NAME  ACCESSION_NO  SOURCE_ID  DISTANCE_UNIT  ORGANISM_ID
-------------------------------------------------------------------------------
28          Wm82.a4.v1    Wm82.a4.v1    Phytozome  bp             3847

1 mapset

Note, the command list mapset will help you find MapSetId that is frequently used in the commands.

In the command above, we have used a name pattern -p to filter the results. Entering the "Wm*" lists all map sets beginning with "Wm". 

Verify the Addition of Map Set Trees

A map set tree is a hierarchical tree structure used to efficiently categorize different types of map sets across multiple organisms in an organized fashion. To see where in the map set tree we have placed the new map set, try this:

PS> list mapsettree -p Wm* -l
Glycine max (NodeId:43, OrderNo:0)
  Physical:Wm82.a4.v1 (NodeId:44, MapSetId:28, OrderNo:0)

You can see the structure of the tree and the identifiers of the tree nodes and map sets.

When referencing an existing map set, you can specify it by its MapSetId or by MapSetPath. The map set path in the tree would be shown by using the command 'list path':

PS> list path -p Wm*
/Glycine max/Wm82.a4.v1