The list command is used to list one or more objects (targets) in your Persephone database. The syntax is as follows:

list {target} [-p pattern] [-l] [-i N] [-r] [-t N]

The table below lists the definitions for the list command parameters.

List Command Parameters

Parameter

Required or Optional?

Definition

{target}

Required

A target is the object type you want to list, which can be organisms, sources, mapsets, chromosomes, maps, sequences, tracktree, tracks, studies, qtls, mapsettree, annot_methods, mapping_methods, alignment_runs, runs, marker_types, track_types, map_types, ontology, or xref_db. Note, that a singular form of the target is also accepted.

-p pattern

Optional

Uses a pattern to filter your results. Wildcards (*) are supported.

-l

Optional

Displays the list in the "long listing" format. See Using the Long-Listing Format for more information.

-i N

Optional

Sorts the list by column index number N. (The default is 0.) For example, entering "-i 3" would sort the list by index number 3.

-r

Optional

Sorts the list in reverse order.

-t N

Optional

Lists the top N items. (The default is 0.) For example, entering "-t 5" would list only the top 5 items.

-d

Optional

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

For example, to list all the organisms in your Persephone database enter list organisms as shown below.

PS> list organisms

The following is a typical example of the output.

-1:Unknown                              0:Unknown
3555:Beta vulgaris subsp. vulgaris      3769:Arabidopsis thaliana
3847:Glycine max                        4081:Solanum lycopersicum
4498:Avena sativa                       4555:Setaria italica
4558:Sorghum bicolor                    4565:Triticum aestivum
9606:Homo sapiens                       10090:Mus musculus
15368:Brachypodium distachyon           29760:Vitis vinifera
38727:Panicum virgatum                  39946:Oryza sativa subsp. indica
112509:Hordeum vulgare subsp. vulgare   138011:Brassica napus var. napus
218851:Aquilegia coerulea               311987:Zea mays
311988:Oryza sativa                     339834:Miscanthus spp
        22 organisms

 

Tip

The List command is commonly used in conjunction with the Delete command to delete objects from the Persephone database. See Deleting Loaded Data for an example of using the List and Delete commands together.

Using the Long-Listing Format

If you want to display more information about an object use the "-l" option to display the list in the "long-listing" format. For example, to list all organisms beginning with the letter "b" you would enter the following:

PS> list organisms -p b* -l

The following is a typical List command output.

ID      NAME    TAXONOMY_NUM    COMMON_NAME     DICOT   ALTERNATIVE_ID
-------------------------------------------------------------------------------
3555    Beta vulgaris subsp. vulgaris   3555    Beta vulgaris subsp. vulgaris
1
15368   Brachypodium distachyon 15368   Brachypodium    0
138011  Brassica napus var. napus       138011  Brassica napus var. napus
1
        3 organisms
PS>

Listing Track Trees

Use the list command followed by the tracktree keyword and the MapSetId to list a track tree. This can display useful information for editing a track tree node. The following shows an example of listing track trees in a map set with a MapSetId of "123456".

PS> list tracktree 123456
[1] CDS – Annotation:0
[2] mRNA – Annotation:1
[3] RepeatMasker – Marker: 2
[4] SNP – Marker:3

Listing the Map Set Tree

An organism can have multiple map sets, which are collections of physical or genetic maps The map set tree is a hierarchical tree structure to efficiently categorize different types of map sets across multiple organisms in an organized fashion. The tree features are called "nodes". A node's "parent" is a node one step higher in the hierarchy and lying on the same branch. A node without any parent is called "root" node; a node without any child is called "leaf" node. "Sibling" nodes share the same parent node. The order between sibling nodes is assignable. There are two types of nodes: a node without an assigned map set (red text in the example below) and a node with a map set (blue text below). Note that a map set cannot be assigned on more than one node. To list a map set tree, use command "list mapsettree". The option -l displays node id along with map set ID/type if it exists.

PS> list mapsettree -l
Brachypodium (NodeId:200081224)
  Physical:Brachypodium annotation (NodeId:200081227, MapSetId:200081226)
    Scaffold:Brachypodium scaffolds (NodeId:200590610, MapSetId:200590609)
  Genetic:Bd3-1 x Bd21 (NodeId:270702460, MapSetId:270702459)