Verify Addition of Maps, Map Sets, and Map Set Trees

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