net.maizegenetics.pangenome.db_loading

Class LoadHapSequencesToDBPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.db_loading.LoadHapSequencesToDBPlugin

All Implemented Interfaces:

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

public class LoadHapSequencesToDBPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

This method takes data processed through GATK haplotype caller, or through processAssebmlyGenomes.Minimap2PipelinePlugin. In either case, the data is subsequently run through ComputeMedianGVCFAndFilter which creates a fasta for loading into the DB via this method. The ID line in the fasta is used to associate each sequence with a DB genome interval id. Entries are added to the following tables for each haplotype: - genotypes - gametes - gamete_groups (only the single taxa/chromosome in each group) - gamete_haplotypes (associates gamete_grp_id to the gamete_id) - haplotypes (sequence related data for each genome_interval for the specified gamete is added) INPUT: 1. configuration file indicating db connection data 2. a fasta file with haplotype anchor sequences. Fasta idlines look as below. >refChrom:refstart:refEnd gvcfFileName 3. a tab-delimited file containing parameters specific for this haplotype, columns are: Genotype/Hapnumber/Dataline/ploidy/reference/genesPhased/chromsPhased/confidence/Method/MethodDetails/RefVersion 4. Path to directory containing the gvcf file OUTPUT: Data is written to the db tables listed above.

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
LoadHapSequencesToDBPlugin()
LoadHapSequencesToDBPlugin(Frame parentFrame)
LoadHapSequencesToDBPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	fasta() Fasta file containing haplotype sequences
LoadHapSequencesToDBPlugin	fasta(String value) Set Fasta File.
String	genomeData() Path to tab-delimited file containing genome speciic data with header line: Genotype Hapnumber Dataline Ploidy Reference GenePhased ChromPhased Confidence Method MethodDetails RefVersion
LoadHapSequencesToDBPlugin	genomeData(String value) Set Genome Data File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	gvcf() GVCF file used to create the haplotype fasta file
LoadHapSequencesToDBPlugin	gvcf(String value) Set GVCF File.
void	postProcessParameters()
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

LoadHapSequencesToDBPlugin

public LoadHapSequencesToDBPlugin()

LoadHapSequencesToDBPlugin

public LoadHapSequencesToDBPlugin(Frame parentFrame)

LoadHapSequencesToDBPlugin

public LoadHapSequencesToDBPlugin(Frame parentFrame,
                                  boolean isInteractive)

Method Detail

postProcessParameters

public void postProcessParameters()

Overrides:

postProcessParameters in class net.maizegenetics.plugindef.AbstractPlugin

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

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

fasta

public String fasta()

Fasta file containing haplotype sequences

Returns:

Fasta File

fasta

public LoadHapSequencesToDBPlugin fasta(String value)

Set Fasta File. Fasta file containing haplotype sequences

Parameters:

value - Fasta File

Returns:

this plugin

genomeData

public String genomeData()

Path to tab-delimited file containing genome speciic data with header line: Genotype Hapnumber Dataline Ploidy Reference GenePhased ChromPhased Confidence Method MethodDetails RefVersion

Returns:

Genome Data File

genomeData

public LoadHapSequencesToDBPlugin genomeData(String value)

Set Genome Data File. Path to tab-delimited file containing genome speciic data with header line: Genotype Hapnumber Dataline Ploidy Reference GenePhased ChromPhased Confidence Method MethodDetails RefVersion

Parameters:

value - Genome Data File

Returns:

this plugin

gvcf

public String gvcf()

GVCF file used to create the haplotype fasta file

Returns:

GVCF File

gvcf

public LoadHapSequencesToDBPlugin gvcf(String value)

Set GVCF File. GVCF file used to create the haplotype fasta file

Parameters:

value - GVCF File

Returns:

this plugin