net.maizegenetics.pangenome.processAssemblyGenomes

Class CreateContigFastaFromAssemblyGenomePlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class CreateContigFastaFromAssemblyGenomePlugin
extends net.maizegenetics.plugindef.AbstractPlugin

The sequence for each chromosome in the genome fasta file will be split based on N's. Read until an N is encountered, write the sequence as its own contig in the contig fastq output file. Skip past the "N's", start the next contig. This algorithm is subject to change during pipeline testing. Each sequence idline will be >assemblyChrom:assemblyStart:assemblyEnd INPUT: 1. The assembly genome file to process OUTPUT: 1. The newly created fasta file of contigs.

Author:

lcj34

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
CreateContigFastaFromAssemblyGenomePlugin()
CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame)
CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	assembly() Output fastq file to use as input for BWA-MEM
CreateContigFastaFromAssemblyGenomePlugin	assembly(String value) Set Output File.
String	genomeFile() Input assembly genome file from which to pull sequence
CreateContigFastaFromAssemblyGenomePlugin	genomeFile(String value) Set Assembly Genome.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	outputDir() Output fastq file to use as input for BWA-MEM
CreateContigFastaFromAssemblyGenomePlugin	outputDir(String value) Set Output File.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

CreateContigFastaFromAssemblyGenomePlugin

public CreateContigFastaFromAssemblyGenomePlugin()

CreateContigFastaFromAssemblyGenomePlugin

public CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame)

CreateContigFastaFromAssemblyGenomePlugin

public CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame,
                                                 boolean isInteractive)

Method Detail

processData

public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

genomeFile

public String genomeFile()

Input assembly genome file from which to pull sequence

Returns:

Assembly Genome

genomeFile

public CreateContigFastaFromAssemblyGenomePlugin genomeFile(String value)

Set Assembly Genome. Input assembly genome file from which to pull sequence

Parameters:

value - Assembly Genome

Returns:

this plugin

assembly

public String assembly()

Output fastq file to use as input for BWA-MEM

Returns:

Output File

assembly

public CreateContigFastaFromAssemblyGenomePlugin assembly(String value)

Set Output File. Output fastq file to use as input for BWA-MEM

Parameters:

value - Output File

Returns:

this plugin

outputDir

public String outputDir()

Output fastq file to use as input for BWA-MEM

Returns:

Output File

outputDir

public CreateContigFastaFromAssemblyGenomePlugin outputDir(String value)

Set Output File. Output fastq file to use as input for BWA-MEM

Parameters:

value - Output File

Returns:

this plugin

getIcon

public ImageIcon getIcon()