Sequencing Variants Toolset

Associated Constructors

Sequencing Variants Toolset

Syntax: Sequencing Variants Toolset

Description: Provides a framework to process and analyze high-throughput sequencing data with SamTools and BcfTools.

Item Messages

Arguments

Syntax: obj << Arguments

Description: Enables specification of options to run the platform from the scripting window.

Run Cmd

Syntax: obj << Run Cmd

Description: Determines the sequencing variants toolset task to be run from the scripting window.

Run Spec

Syntax: obj << Run Spec

Description: Determines the sequencing variants toolset task to be run from the interface window.

Specification

Syntax: obj << Specification

Description: Enables specification of a task.

Shared Item Messages

Action

Syntax: obj << Action

Description: All-purpose trapdoor within a platform to insert expressions to evaluate. Temporarily sets the DisplayBox and DataTable contexts to the Platform.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Bivariate(
    Y( :height ),
    X( :weight ),
    Action( Distribution( Y( :height, :weight ), Histograms Only ) )
);

Apply Preset

Syntax: Apply Preset( preset ); Apply Preset( source, label, <Folder( folder {, folder2, ...} )> )

Description: Apply a previously created preset to the object, updating the options and customizations to match the saved settings.

JMP Version Added: 18

Anonymous preset

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :height ), X( :sex ), t Test( 1 ) );
preset = obj << New Preset();
dt2 = Open( "$SAMPLE_DATA/Dogs.jmp" );
obj2 = dt2 << Oneway( Y( :LogHist0 ), X( :drug ) );
Wait( 1 );
obj2 << Apply Preset( preset );

Search by name

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :height ), X( :sex ) );
Wait( 1 );
obj << Apply Preset( "Sample Presets", "Compare Distributions" );

Search within folder(s)

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :height ), X( :sex ) );
Wait( 1 );
obj << Apply Preset( "Sample Presets", "t-Tests", Folder( "Compare Means" ) );

Copy Script

Syntax: obj << Copy Script

Description: Create a JSL script to produce this analysis, and put it on the clipboard.

obj << Copy Script;

Get By Levels

Syntax: obj << Get By Levels

Description: Returns an associative array mapping the by group columns to their values.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
biv = dt << Bivariate( X( :height ), Y( :weight ), By( :sex ) );
biv << Get By Levels;

Get Container

Syntax: obj << Get Container

Description: Returns a reference to the container box that holds the content for the object.

General

t = obj << Get Container;
Show( (t << XPath( "//OutlineBox" )) << Get Title );

Platform with Filter

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
gb = Graph Builder(
    Show Control Panel( 0 ),
    Variables( X( :height ), Y( :weight ) ),
    Elements( Points( X, Y, Legend( 1 ) ), Smoother( X, Y, Legend( 2 ) ) ),
    Local Data Filter(
        Add Filter(
            columns( :age, :sex, :height ),
            Where( :age == {12, 13, 14} ),
            Where( :sex == "F" ),
            Where( :height >= 55 ),
            Display( :age, N Items( 6 ) )
        )
    )
);
New Window( "platform boxes",
    H List Box(
        Outline Box( "Report(platform)", Report( gb ) << Get Picture ),
        Outline Box( "platform << Get Container", (gb << Get Container) << Get Picture )
    )
);

Get Data Table

Syntax: obj << Get Data Table

Description: Returns a reference to the data table.

t = obj << Get Datatable;
Show( N Rows( t ) );

Get Script

Syntax: obj << Get Script

Description: Creates a script (JSL) to produce this analysis and returns it as an expression.

t = obj << Get Script;
Show( t );

Get Script With Data Table

Syntax: obj << Get Script With Data Table

Description: Creates a script(JSL) to produce this analysis specifically referencing this data table and returns it as an expression.

t = obj << Get Script With Data Table;
Show( t );

Get Timing

Syntax: obj << Get Timing

Description: Times the platform launch.

t = obj << Get Timing;
Show( t );

Get Web Support

Syntax: obj << Get Web Support

Description: Return a number indicating the level of Interactive HTML support for the display object. 1 means some or all elements are supported. 0 means no support.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Bivariate( Y( :Weight ), X( :Height ) );
s = obj << Get Web Support();
Show( s );

Get Where Expr

Syntax: obj << Get Where Expr

Description: Returns the Where expression for the data subset, if the platform was launched with By() or Where(). Otherwise, returns Empty()

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
biv = dt << Bivariate( X( :height ), Y( :weight ), By( :sex ) );
biv2 = dt << Bivariate( X( :height ), Y( :weight ), Where( :age < 14 & :height > 60 ) );
Show( biv[1] << Get Where Expr, biv2 << Get Where Expr );

Ignore Platform Preferences

Syntax: Ignore Platform Preferences( state=0|1 )

Description: Ignores the current settings of the platform's preferences. The message is ignored when sent to the platform after creation.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Bivariate(
    Ignore Platform Preferences( 1 ),
    Y( :height ),
    X( :weight ),
    Action( Distribution( Y( :height, :weight ), Histograms Only ) )
);

New JSL Preset

Syntax: New JSL Preset( preset )

Description: For testing purposes, create a preset directly from a JSL expression. Like <<New Preset, it will return a Platform Preset that can be applied using <<Apply Preset. But it allows you to specify the full JSL expression for the preset to test outside of normal operation. You will get an Assert on apply if the platform names do not match, but that is expected.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :Height ), X( :Age ) );
preset = obj << New JSL Preset( Oneway( Y( :A ), X( :B ), Each Pair( 1 ) ) );
Wait( 1 );
obj << Apply Preset( preset );

New Preset

Syntax: obj = New Preset()

Description: Create an anonymous preset representing the options and customizations applied to the object. This object can be passed to Apply Preset to copy the settings to another object of the same type.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :height ), X( :sex ), t Test( 1 ) );
preset = obj << New Preset();

Render Preset

Syntax: Render Preset( preset )

Description: For testing purposes, show the platform rerun script that would be used when applying a platform preset to the platform in the log. No changes are made to the platform.

JMP Version Added: 18

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Oneway( Y( :Height ), X( :Age ) );
obj << Render Preset( Expr( Oneway( Y( :A ), X( :B ), Each Pair( 1 ) ) ) );

Report

Syntax: obj << Report;Report( obj )

Description: Returns a reference to the report object.

r = obj << Report;
t = r[Outline Box( 1 )] << Get Title;
Show( t );

Save Script for All Objects

Syntax: obj << Save Script for All Objects

Description: Creates a script for all report objects in the window and appends it to the current Script window. This option is useful when you have multiple reports in the window.

obj << Save Script for All Objects;

Save Script for All Objects To Data Table

Syntax: obj << Save Script for All Objects To Data Table( <name> )

Description: Saves a script for all report objects to the current data table. This option is useful when you have multiple reports in the window. The script is named after the first platform unless you specify the script name in quotes.

Example 1

obj[1] << Save Script for All Objects To Data Table;

Example 2

obj[1] << Save Script for All Objects To Data Table( "My Script" );

Save Script to Data Table

Syntax: Save Script to Data Table( <name>, < <<Prompt(0|1)>, < <<Replace(0|1)> );

Description: Create a JSL script to produce this analysis, and save it as a table property in the data table.

obj << Save Script to Data Table( "My Analysis", <<Prompt( 0 ), <<Replace( 0 ) );

Save Script to Journal

Syntax: obj << Save Script to Journal

Description: Create a JSL script to produce this analysis, and add a Button to the journal containing this script.

obj << Save Script to Journal;

Save Script to Report

Syntax: obj << Save Script to Report

Description: Create a JSL script to produce this analysis, and show it in the report itself. Useful to preserve a printed record of what was done.

obj << Save Script to Report;

Save Script to Script Window

Syntax: obj << Save Script to Script Window

Description: Create a JSL script to produce this analysis, and append it to the current Script text window.

obj << Save Script to Script Window;

SendToByGroup

Syntax: SendToByGroup( {":Column == level"}, command );

Description: Sends platform commands or display customization commands to each level of a by-group.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Distribution(
    By( :Sex ),
    SendToByGroup(
        {:sex == "F"},
        Continuous Distribution( Column( :weight ), Normal Quantile Plot( 1 ) )
    ),
    SendToByGroup( {:sex == "M"}, Continuous Distribution( Column( :weight ) ) )
);

SendToEmbeddedScriptable

Syntax: SendToEmbeddedScriptable( Dispatch( "Outline name", "Element name", command );

Description: SendToEmbeddedScriptable restores settings of embedded scriptable objects.

dt = Open( "$SAMPLE_DATA/Reliability/Fan.jmp" );
dt << Life Distribution(
    Y( :Time ),
    Censor( :Censor ),
    Censor Code( 1 ),
    <<Fit Weibull,
    SendToEmbeddedScriptable(
        Dispatch(
            {"Statistics", "Parametric Estimate - Weibull", "Profilers", "Density Profiler"},
            {1, Confidence Intervals( 0 ), Term Value( Time( 6000, Lock( 0 ), Show( 1 ) ) )}
        )
    )
);

SendToReport

Syntax: SendToReport( Dispatch( "Outline name", "Element name", Element type, command );

Description: Send To Report is used in tandem with the Dispatch command to customize the appearance of a report.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
dt << Distribution(
    Nominal Distribution( Column( :age ) ),
    Continuous Distribution( Column( :weight ) ),
    SendToReport( Dispatch( "age", "Distrib Nom Hist", FrameBox, {Frame Size( 178, 318 )} ) )
);

Title

Syntax: obj << Title( "new title" )

Description: Sets the title of the platform.

obj << Title( "My Platform" );

Top Report

Syntax: obj << Top Report

Description: Returns a reference to the root node in the report.

r = obj << Top Report;
t = r[Outline Box( 1 )] << Get Title;
Show( t );

View Web XML

Syntax: obj << View Web XML

Description: Returns the XML code that is used to create the interactive HTML report.

dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
obj = dt << Bivariate( Y( :Weight ), X( :Height ) );
xml = obj << View Web XML;

Sequencing Variants Toolset Run

Item Messages

Auto Send Output to Files List

Syntax: obj << Auto Send Output to Files List( state=0|1 )

Description: Sends output files to the files list panel.

Bam Files

Syntax: obj << Bam Files

Description: Specifies BAM files.

Bcf Files

Syntax: obj << Bcf Files

Description: Specifies BCF files.

Caller

Syntax: obj << Caller( "Multiallelic"|"Consensus"="Multiallelic" )

Description: "Multiallelic" by default.

Copy Task Specification

Syntax: obj << Copy Task Specification

Description: Copies the current sequencing variants toolset specifications to the clipboard.

JMP Version Added: 19

Files

Syntax: obj << Files

Description: Load input files to be run in samtools.

Ploidy

Syntax: obj << Ploidy( number=2 )

Description: "2" by default.

Recall in Task Specification

Syntax: obj << Recall in Task Specification

Description: Sets the task specification in the Task Specification report to the specified model.

Ref Files

Syntax: obj << Ref Files

Description: Specifies Reference Genome files.

Remove Run

Syntax: obj << ( Run[number] << Remove Run( state=0|1 ) )

Description: Removes the specified run report from the report window.

Results Folder

Syntax: obj << Results Folder

Description: Specifies the result folder.

Sam Files

Syntax: obj << Sam Files

Description: Specifies SAM files.

Send Output to Files List

Syntax: obj << Send Output to Files List( state=0|1 )

Description: Sends output files to the file list panel.

Sort Reads By

Syntax: obj << Sort Reads By( "Coordinates"|"Alpha-numeric"|"Lexicographical"="Coordinates" )

Description: "Coordinates" by default.

Summary

Syntax: obj << Summary( state=0|1 )

Description: Shows or hides a report that contains details of the run. On by default.

Target Regions

Syntax: obj << Target Regions

Description: Sets target regions. The specification of regions requires that the BAM file be coordinate-sorted and indexed.

Task

Syntax: obj << Task( "Index Fasta"|"Convert SAM to BAM"|"Sort Reads"|"Add Mate Coordinates"|"Remove Duplicates"|"Merge Files"|"Index BAM"|"Convert BAM To SAM"|"Extract Mapped Reads"|"Extract Unmapped Reads"|"Extract Target Regions"|"Extract Properly Aligned"|"Extract First Read"|"Tag Mismatches and Insertions"|"Count Alignment"|"Count Alignment By Flag"|"Count Alignment By Reference"|"Generate Statistics"|"Generate Base Alignment Quality"|"Generate Read Depth"|"Bgzip Compress"|"Bgzip Decompress"|"Generate Genotype Likelihoods"|"Generate Genotype Calls"|"Convert Bcf to Vcf"|"Convert Vcf to Bcf" )

Description: Determines the task to run.

Title

Syntax: obj << Title

Description: Sets a title.

Unthreaded

Syntax: obj << Unthreaded( state=0|1 )

Description: Use only the main thread for calculations

Vcf Files

Syntax: obj << Vcf Files

Description: Specifies VCF files.

Sequencing Variants Toolset Specification

Item Messages

Auto Send Output to Files List

Syntax: obj << Auto Send Output to Files List( state=0|1 )

Description: Sends output files to the files list panel.

Bam Files

Syntax: obj << Bam Files

Description: Specifies BAM files.

Bcf Files

Syntax: obj << Bcf Files

Description: Specifies BCF files.

Caller

Syntax: obj << Caller( "Multiallelic"|"Consensus"="Multiallelic" )

Description: "Multiallelic" by default.

Files

Syntax: obj << Files

Description: Load input files to be run in samtools.

Ploidy

Syntax: obj << Ploidy( number=2 )

Description: Specifies a positive number that indicates the ploidy level. "2" by default.

Ref Files

Syntax: obj << Ref Files

Description: Specifies Reference Genome files.

Results Folder

Syntax: obj << Results Folder

Description: Specifies the result folder.

Sam Files

Syntax: obj << Sam Files

Description: Specifies SAM files.

Sort Reads By

Syntax: obj << Sort Reads By( "Coordinates"|"Alpha-numeric"|"Lexicographical"="Coordinates" )

Description: "Coordinates" by default.

Target Regions

Syntax: obj << Target Regions

Description: Sets target regions. The specification of regions requires that the BAM file be coordinate-sorted and indexed.

Task

Syntax: obj << Task( "Index Fasta"|"Convert SAM to BAM"|"Sort Reads"|"Add Mate Coordinates"|"Remove Duplicates"|"Merge Files"|"Index BAM"|"Convert BAM To SAM"|"Extract Mapped Reads"|"Extract Unmapped Reads"|"Extract Target Regions"|"Extract Properly Aligned"|"Extract First Read"|"Tag Mismatches and Insertions"|"Count Alignment"|"Count Alignment By Flag"|"Count Alignment By Reference"|"Generate Statistics"|"Generate Base Alignment Quality"|"Generate Read Depth"|"Bgzip Compress"|"Bgzip Decompress"|"Generate Genotype Likelihoods"|"Generate Genotype Calls"|"Convert Bcf to Vcf"|"Convert Vcf to Bcf"="Index Fasta" )

Description: Determines the task to run. "Index Fasta" by default.

Title

Syntax: obj << Title

Description: Sets a title.

Unthreaded

Syntax: obj << Unthreaded( state=0|1 )

Description: Use only the main thread for calculations

Vcf Files

Syntax: obj << Vcf Files

Description: Specifies VCF files.