net.maizegenetics.pangenome.db_loading

Class LoadConsensusAnchorSequencesPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.db_loading.LoadConsensusAnchorSequencesPlugin

All Implemented Interfaces:

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

public class LoadConsensusAnchorSequencesPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

This method takes an input file in fasta format and adds the sequences to the data base. The fasta file's idline must be of the format: > refChrom:refStartPos:refEndPos;TaxaName_hapNumber:TaxaName2_hapNumber:... gvcfFile A semi-colon separates the ref coordinates from the list of taxa. The ref coordinates are used to identify the anchor to which the sequence belongs. The taxa names indicate the taxa (haplotypes) whose sequences at the indicated anchor collapse to this consensus. A space separates the taxaNames from the gvcf file. This should be gvcf name only. The directory containing the gvcfs is a plugin parameter. The names on the taxa list must consist of the genotype line name as stored in the genotypes table line_name field connect with an underscore to the hap number for this line. This allows identifying the haplotype id stored in the db. INPUT: 1. the config file with specifics for connection to the db 2. a fasta file of consensus anchor sequences 3. name of anchor version as stored in the db. This identifies anchors is different sets were loaded. 4. name of method used to collapse anchors. Can be an existing method or a new one. 5. String explaining the collapsing algorithm used. Can be empty (which would imply this already exists) OUTPUT: Data is written to the following PHG tables: 1. gamete_groups 2. gamete_haplotypes 3. haplotypes NOTE: Files are processed in batches to facilitate being called from the RunHapCollapsePipeline, which creates a separate file for every anchor/ref-range (37804 for maize).

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
LoadConsensusAnchorSequencesPlugin()
LoadConsensusAnchorSequencesPlugin(Frame parentFrame)
LoadConsensusAnchorSequencesPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	collapseMethod() Name of method used to collapse the anchors.
LoadConsensusAnchorSequencesPlugin	collapseMethod(String value) Set Collapse Method.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	inputFile() Input fasta file with consensus sequences
LoadConsensusAnchorSequencesPlugin	inputFile(String value) Set Input File.
String	methodDetails() Description of methods used to collapse the anchor sequences.
LoadConsensusAnchorSequencesPlugin	methodDetails(String value) Set Collapse Method Description.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	vcfDir() Directory containing vcf files for consensus sequences.
LoadConsensusAnchorSequencesPlugin	vcfDir(String value) Set VCF Directory.
String	version() Version name for this set of anchors as stored in anchor_versions table in db
LoadConsensusAnchorSequencesPlugin	version(String value) Set Anchor Version.

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

LoadConsensusAnchorSequencesPlugin

public LoadConsensusAnchorSequencesPlugin()

LoadConsensusAnchorSequencesPlugin

public LoadConsensusAnchorSequencesPlugin(Frame parentFrame)

LoadConsensusAnchorSequencesPlugin

public LoadConsensusAnchorSequencesPlugin(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

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

inputFile

public String inputFile()

Input fasta file with consensus sequences

Returns:

Input File

inputFile

public LoadConsensusAnchorSequencesPlugin inputFile(String value)

Set Input File. Input fasta file with consensus sequences

Parameters:

value - Input File

Returns:

this plugin

version

public String version()

Version name for this set of anchors as stored in anchor_versions table in db

Returns:

Anchor Version

version

public LoadConsensusAnchorSequencesPlugin version(String value)

Set Anchor Version. Version name for this set of anchors as stored in anchor_versions table in db

Parameters:

value - Anchor Version

Returns:

this plugin

vcfDir

public String vcfDir()

Directory containing vcf files for consensus sequences.

Returns:

value VCF Directory

vcfDir

public LoadConsensusAnchorSequencesPlugin vcfDir(String value)

Set VCF Directory.

Parameters:

value -

Returns:

collapseMethod

public String collapseMethod()

Name of method used to collapse the anchors. If it doesn't exist, will be added to methods table.

Returns:

Collapse Method

collapseMethod

public LoadConsensusAnchorSequencesPlugin collapseMethod(String value)

Set Collapse Method. Name of method used to collapse the anchors. If it doesn't exist, will be added to methods table.

Parameters:

value - Collapse Method

Returns:

this plugin

methodDetails

public String methodDetails()

Description of methods used to collapse the anchor sequences.

Returns:

Collapse Method Description

methodDetails

public LoadConsensusAnchorSequencesPlugin methodDetails(String value)

Set Collapse Method Description. Description of methods used to collapse the anchor sequences.

Parameters:

value - Collapse Method Description

Returns:

this plugin