Package ubic.gemma.apps

Class ArrayDesignProbeMapperCli

java.lang.Object

ubic.gemma.cli.util.AbstractCLI

ubic.gemma.cli.util.AbstractAuthenticatedCLI

ubic.gemma.cli.util.AbstractAutoSeekingCLI<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

arrayDesignReportService, arrayDesignService, 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	buildArrayDesignOptions(org.apache.commons.cli.Options options)
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, ArrayDesign arrayDesign, Class<? extends ArrayDesignAnalysisEvent> eventClass)	Override to do additional checks to make sure the array design is in a state of readiness for probe mapping.
protected void	processArrayDesignOptions(org.apache.commons.cli.CommandLine commandLine)	See 'configure' for how the other options are handled.
protected void	processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)

Methods inherited from class ubic.gemma.apps.ArrayDesignSequenceManipulatingCli

buildOptions, doAuthenticatedWork, getCommandGroup, getRelatedDesigns, isSubsumedOrMerged, processArrayDesign, processOptions, 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, doWork, setAuthenticateAnonymously, 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, getBatchTaskProgressReporter, 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 Details

ArrayDesignProbeMapperCli

public ArrayDesignProbeMapperCli()

Method Details

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

buildArrayDesignOptions

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

Overrides:

buildArrayDesignOptions in class ArrayDesignSequenceManipulatingCli

processArrayDesignOptions

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

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

Overrides:

processArrayDesignOptions in class ArrayDesignSequenceManipulatingCli

Throws:

org.apache.commons.cli.ParseException

needToRun

protected boolean needToRun(Date skipIfLastRunLaterThan,
 ArrayDesign arrayDesign,
 Class<? extends 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

Parameters:

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.

processArrayDesigns

protected void processArrayDesigns(Collection<ArrayDesign> arrayDesignsToProcess)

Overrides:

processArrayDesigns in class ArrayDesignSequenceManipulatingCli