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- All Implemented Interfaces:
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java.lang.Runnable
,net.maizegenetics.plugindef.Plugin
,net.maizegenetics.plugindef.PluginListener
,net.maizegenetics.util.ProgressListener
public class CreateContigFastaFromAssemblyGenomePlugin extends 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.
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Field Summary
Fields Modifier and Type Field Description public final static String
DEFAULT_CITATION
public final static String
POSITION_LIST_NONE
public final static String
TAXA_LIST_NONE
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Constructor Summary
Constructors Constructor Description CreateContigFastaFromAssemblyGenomePlugin()
CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame)
CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame, boolean isInteractive)
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Method Summary
Modifier and Type Method Description DataSet
processData(DataSet input)
String
getButtonName()
String
getToolTipText()
String
genomeFile()
Input assembly genome file from which to pull sequence CreateContigFastaFromAssemblyGenomePlugin
genomeFile(String value)
Set Assembly Genome. String
assembly()
Output fastq file to use as input for BWA-MEM CreateContigFastaFromAssemblyGenomePlugin
assembly(String value)
Set Output File. String
outputDir()
Output fastq file to use as input for BWA-MEM CreateContigFastaFromAssemblyGenomePlugin
outputDir(String value)
Set Output File. ImageIcon
getIcon()
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Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin
addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getListeners, getMenu, getPanel, getParameter, getParentFrame, getUsage, getUsageHTML, hasListeners, isInteractive, isPluginParameter, performFunction, pluginDescription, pluginParameters, pluginUserManualURL, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameters, setParametersToDefault, setThreaded, trace, usageParameters, wasCancelled
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Methods inherited from class net.maizegenetics.plugindef.Plugin
getPluginInstance, isPlugin
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Constructor Detail
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CreateContigFastaFromAssemblyGenomePlugin
CreateContigFastaFromAssemblyGenomePlugin()
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CreateContigFastaFromAssemblyGenomePlugin
CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame)
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CreateContigFastaFromAssemblyGenomePlugin
CreateContigFastaFromAssemblyGenomePlugin(Frame parentFrame, boolean isInteractive)
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Method Detail
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processData
DataSet processData(DataSet input)
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getButtonName
String getButtonName()
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getToolTipText
String getToolTipText()
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genomeFile
String genomeFile()
Input assembly genome file from which to pull sequence
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genomeFile
CreateContigFastaFromAssemblyGenomePlugin genomeFile(String value)
Set Assembly Genome. Input assembly genome file from which to pull sequence
- Parameters:
value
- Assembly Genome
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assembly
CreateContigFastaFromAssemblyGenomePlugin assembly(String value)
Set Output File. Output fastq file to use as input for BWA-MEM
- Parameters:
value
- Output File
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outputDir
CreateContigFastaFromAssemblyGenomePlugin outputDir(String value)
Set Output File. Output fastq file to use as input for BWA-MEM
- Parameters:
value
- Output File
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