The table below lists the supported and unsupported commands in PersephoneShell. For commands with simple syntax refer to the Syntax column. For commands with more complex syntax you can also click the command's name in the Command column for more information.

Supported and Unsupported Commands in PersephoneShell

Command

Description

Syntax

Comments

Add

Add object(s) to the Persephone database.

add {target} -c controlFile [(-v | -t) -d]

A target is required. Valid targets: organism, sequence(s), map(s), annotation(s), marker(s), alignment(s),  synteny, mapsettreenode, expression, variant(s), quantitative, tracktreenode, qtl(s), ortholog(s) or ontology.

Clear

Clear screen.

clear

 

Convert

N/A

N/A

This command is not currently supported.

Delete

Delete object(s) from the database.

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

A target is required. Valid targets: mapsettreenode, tracktreenode, organism, mapset, run, map, storage, alignment_run

Edit

Edit selected object

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

A target is required. Valid targets: mapsettreenode, tracktreenode.

Help

Display a list of commands.

help

 

History

Display a list of commands that has been entered.

history

 

Init

Initializes the Persephone database schema.

init [(-v | -t) | -d]

See Initializing the Schema for more information.

List

Lists one or more objects in the Persephone database.

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

A target is required. Valid targets: organisms, mapsets, chromosomes, maps, sequences, tracktree, tracks, studies, qtls, mapsettree, annot_methods, mapping_methods, alignment_runs, runs, marker_types, track_types, map_types, ontology, xref_db.

Quit (Exit)

Exit PersephoneShell.

quit
or
exit

 

Update

Updates the data stored in the old format, taking advantage of the new format

update {target} {id|path} [-d]

Target: quantitative. The old data for quantitative tracks will be processed to enable using the new format (populating an extra column in the database).

 

Tip

For most commands if you enter it without any parameters it will display the correct syntax.

Auto Completing Commands and Command Parameters

You can auto complete commands by entering one or more characters and then pressing the Tab key. In addition, you can auto complete targets, file paths, map set paths, and track paths just by pressing the Tab key and scrolling through all the possible choices. See Auto Completing Commands and Command Parameters for more information.

Optional Command Parameters

Several PersephoneShell commands support optional parameters to help you view, test, and debug commands. These parameters are described below. Please refer to the specific command section (e.g., Add) to see which parameters (if any) are supported.

Debug Parameter (-d and --debugMode)

PersephoneShell displays any error and relevant options in a user-friendly format. However, using either the –d or --debugMode parameter will show application messages the developers at Persephone Software, LLC. can use to quickly diagnose problems. Please send debug reports to us http://persephonesoft.com/contact so we can help you analyze the issue.

The following is an example of using the debug parameter with the add command.

PS> add synteny -c add_hg19_mm10_gff.ini -d

Verbose Parameter (-v or --verboseMode)

You can use either the -v or --verboseMode parameter on some commands to display detailed messages in real time as the command executes. If a command executes successfully but in a way you did not expect, for example, you can use the verbose parameter to see how and why it performed as it did.

The following is an example of using the verbose parameter with the add command.

PS> add synteny -c add_hg19_mm10_gff.ini -v

 

Note

Sometimes, if you use the verbose parameter you cannot use the test parameter (described below).

Test Parameter (-t)

You can use the test parameter (-t) to put a command in the test mode, where a set of checklist items is validated and prints out the results as "passed" or "failed". Any failed item will produce an exception in normal mode. This can help you narrow down any issues you may be having with a command.

The following is an example of using the test parameter with the add command.

PS> add synteny -c add_hg19_mm10_gff.ini -t

 

Note

It is very common (and recommended) to run a command in the test mode first and then, if the test succeeds, run it with the verbose parameter.