Package ubic.gemma.apps

Class ArrayDesignProbeMapperCli

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.cli.util.AbstractAutoSeekingCLI<ubic.gemma.model.expression.arrayDesign.ArrayDesign>

ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

ubic.gemma.apps.ArrayDesignProbeMapperCli

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.beans.factory.InitializingBean, org.springframework.context.ApplicationContextAware, org.springframework.context.EnvironmentAware, CLI

public class ArrayDesignProbeMapperCli
extends ArrayDesignSequenceManipulatingCli

Process the blat results for an array design to map them onto genes. Typical workflow would be to run:

1. Create the array design, perhaps by loading a GPL or via a GSE.
2. ArrayDesignSequenceAssociationCli - attach sequences to array design, fetching from BLAST database if necessary. For affymetrix designs, get the probe sequences and pass them to the command line (also a web interface)
3. ArrayDesignBlatCli - runs blat. You must start the appropriate server using the configuration in the properties files.
4. ArrayDesignProbeMapperCli (this class); you must have the correct GoldenPath database installed and available as configured in your properties files.

This can also allow directly associating probes with genes (via products) based on an input file, without any sequence analysis.

In batch mode, platforms that are "children" (mergees or subsumees) of other platforms will be skipped. Platforms which are themselves merged or subsumers, when run, will result in the child platforms being updated implicitly (via an audit event and report update)

Author:

pavlidis

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.cli.util.CLI

CLI.CommandGroup

Field Summary

Fields inherited from class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

auditEventService, auditTrailService, entityLocator

Fields inherited from class ubic.gemma.cli.util.AbstractAutoSeekingCLI

FORCE_OPTION

Fields inherited from class ubic.gemma.cli.util.AbstractCLI

ABORTED, FAILURE, FAILURE_FROM_ERROR_OBJECTS, log, SUCCESS

Constructor Summary

Constructors

Constructor	Description
ArrayDesignProbeMapperCli()

Method Summary

Modifier and Type	Method	Description
protected void	buildOptions(org.apache.commons.cli.Options options)	Build option implementation.
protected void	doAuthenticatedWork()
String	getCommandName()	A short memorable name for the command that can be used to locate this class.
String	getShortDesc()	Obtain a short description for this command explaining what it does.
protected boolean	needToRun(Date skipIfLastRunLaterThan, ubic.gemma.model.expression.arrayDesign.ArrayDesign arrayDesign, Class<? extends ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent> eventClass)	Override to do additional checks to make sure the array design is in a state of readiness for probe mapping.
protected void	processOptions(org.apache.commons.cli.CommandLine commandLine)	See 'configure' for how the other options are handled.

Methods inherited from class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

getArrayDesignReportService, getArrayDesignService, getArrayDesignsToProcess, getCommandGroup, isSubsumedOrMerged, shouldRun, toBatchObject

Methods inherited from class ubic.gemma.cli.util.AbstractAutoSeekingCLI

addAutoOption, addAutoOption, addErrorObject, addErrorObject, addErrorObject, addForceOption, addForceOption, addLimitingDateOption, addSuccessObject, addSuccessObject, addWarningObject, addWarningObject, getAutoSeekEventType, getLimitingDate, isAutoSeek, isForce, noNeedToRun, setForce

Methods inherited from class ubic.gemma.cli.util.AbstractAuthenticatedCLI

afterPropertiesSet, createBatchTaskExecutorService, doWork, setEnvironment, setRequireLogin

Methods inherited from class ubic.gemma.cli.util.AbstractCLI

abort, addBatchOption, addErrorObject, addErrorObject, addErrorObject, addSuccessObject, addSuccessObject, addThreadsOption, addWarningObject, addWarningObject, allowPositionalArguments, awaitBatchExecutorService, executeCommand, getApplicationContext, getBatchTaskExecutor, getCliContext, getCommandAliases, getHelpFooter, getNumThreads, getOptions, getUsage, promptConfirmationOrAbort, setAllowPositionalArguments, setApplicationContext, setEstimatedMaxTasks, setReportFrequencyMillis

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ArrayDesignProbeMapperCli

public ArrayDesignProbeMapperCli()

Method Detail

getShortDesc

public String getShortDesc()

Description copied from interface: CLI

Obtain a short description for this command explaining what it does.

Specified by:

getShortDesc in interface CLI

Overrides:

getShortDesc in class AbstractCLI

buildOptions

protected void buildOptions(org.apache.commons.cli.Options options)

Description copied from class: AbstractCLI

Build option implementation.

Implement this method to add options to your command line, using the OptionBuilder.

This is called right after AbstractCLI.buildStandardOptions(Options) so the options will be added after standard options.

Overrides:

buildOptions in class ArrayDesignSequenceManipulatingCli

processOptions

protected void processOptions(org.apache.commons.cli.CommandLine commandLine)
                       throws org.apache.commons.cli.ParseException

See 'configure' for how the other options are handled. (non-Javadoc)

Overrides:

processOptions in class ArrayDesignSequenceManipulatingCli

Throws:

org.apache.commons.cli.ParseException - in case of unrecoverable failure (i.e. missing option or invalid value), an exception can be raised and will result in an exit code of AbstractCLI.FAILURE.

See Also:

AbstractCLI.processOptions(CommandLine)

needToRun

protected boolean needToRun(Date skipIfLastRunLaterThan,
                            ubic.gemma.model.expression.arrayDesign.ArrayDesign arrayDesign,
                            Class<? extends ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignAnalysisEvent> eventClass)

Override to do additional checks to make sure the array design is in a state of readiness for probe mapping.

Overrides:

needToRun in class ArrayDesignSequenceManipulatingCli

eventClass - e.g., ArrayDesignSequenceAnalysisEvent.class

Returns:

true if skipIfLastRunLaterThan is null, or there is no record of a previous analysis, or if the last analysis was run before skipIfLastRunLaterThan. false otherwise.

getCommandName

public String getCommandName()

Description copied from interface: CLI

A short memorable name for the command that can be used to locate this class.

Specified by:

getCommandName in interface CLI

Overrides:

getCommandName in class AbstractCLI

Returns:

name; if null or blank, this will not be available as a shortcut command.

doAuthenticatedWork

protected void doAuthenticatedWork()
                            throws Exception

Specified by:

doAuthenticatedWork in class AbstractAuthenticatedCLI

Throws:

Exception