net.maizegenetics.pangenome.db_loading

Class SplitFastaByChromPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

All Implemented Interfaces:

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

public class SplitFastaByChromPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Splits fasta by chromosome. IT assumes the id line has a chromosome of the form >1, >chr1 or >chromosome1 ALl of the above forms (case insensitive) will be written with an id line of just the number, e.g. >1 or >2 The "name" parameter is used as the basis of the name. To this name will be appended the "chr" and chrom number and .fa. For example: If the user gives "w22" as the name, the code will write files: w22chr1.fa, w22chr2.fa, etc. The isGca parameter: The assemblies starting with GCA have long text in the idLIne, with the chromosome stuck in the middle. This plugin will correctly parse these lines. OTher weird id lines are not supported and may need to be corrected manually before running through this plugin.

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
SplitFastaByChromPlugin()
SplitFastaByChromPlugin(Frame parentFrame)
SplitFastaByChromPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	fasta() Fasta File to split by chromosome
SplitFastaByChromPlugin	fasta(String value) Set Fasta File .
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
Boolean	isGca() GCA fastas have long text as idLines.
SplitFastaByChromPlugin	isGca(Boolean value) Set Is GCA.
static void	main(String[] args)
String	name() Name to give each file, e.g w22.
SplitFastaByChromPlugin	name(String value) Set Name .
String	outputDir() Path to write the split files
SplitFastaByChromPlugin	outputDir(String value) Set Output Directory.
String	parseGCA(String chromString)
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

SplitFastaByChromPlugin

public SplitFastaByChromPlugin()

SplitFastaByChromPlugin

public SplitFastaByChromPlugin(Frame parentFrame)

SplitFastaByChromPlugin

public SplitFastaByChromPlugin(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

parseGCA

public String parseGCA(String chromString)

main

public static void main(String[] args)

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

fasta

public String fasta()

Fasta File to split by chromosome

Returns:

Fasta File

fasta

public SplitFastaByChromPlugin fasta(String value)

Set Fasta File . Fasta File to split by chromosome

Parameters:

value - Fasta File

Returns:

this plugin

name

public String name()

Name to give each file, e.g w22. To this name will be appended 'chr' plus the chrom number plus .fa

Returns:

Name

name

public SplitFastaByChromPlugin name(String value)

Set Name . Name to give each file, e.g w22. To this name will be appended 'chr' plus the chrom number plus .fa

Parameters:

value - Name

Returns:

this plugin

outputDir

public String outputDir()

Path to write the split files

Returns:

Output Directory

outputDir

public SplitFastaByChromPlugin outputDir(String value)

Set Output Directory. Path to write the split files

Parameters:

value - Output Directory

Returns:

this plugin

isGca

public Boolean isGca()

GCA fastas have long text as idLines. These fasta will have their id lines specially parsed to extract the chromosome number.

Returns:

Is GCA

isGca

public SplitFastaByChromPlugin isGca(Boolean value)

Set Is GCA. GCA fastas have long text as idLines. These fasta will have their id lines specially parsed to extract the chromosome number.

Parameters:

value - Is GCA

Returns:

this plugin