net.maizegenetics.pangenome.db_loading

Class LoadGenomeIntervalsToPHGdbPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.db_loading.LoadGenomeIntervalsToPHGdbPlugin

All Implemented Interfaces:

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

public class LoadGenomeIntervalsToPHGdbPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Before running this plugin, GetDBConnectionPlugin must be run. The connection created by GetDBConnectionPlugin is passed as a DataSet parameter to this plugin. This Plugin takes an anchorsFile indicating chrom, start, end, and a reference genome. It creates anchors from the ref genome fasta based on the start/end from the anchorsFile and loads them to the specified PHG database. The genome data file contains details to be added to the genotypes, gametes and method tables. When finished loading anchor regions, inter-anchor regions are identified and loaded. INPUT: 1. anchors file: tab delimited file, header lines begin with #: data lines have columns for chr,startpos,endpos (other columns may be present but will be ignored) 2. path to reference genome fasta file 3. Tab delimited file containing genome data with columns: Genotype Hapnumber Dataline Ploidy Reference GenesPhased ChromsPhased Confidence Method MethodDetails RefVersion The RefVersion will be stored in the genome_interval_versions table. The Method and MethodDetails will be stored in the methods table. The MethodDetails will also be stored in the description field of the genome_interval_versions table. HapNumber starts with 0, and should be 0 for the reference line and all inbreds. OUTPUT: 1. database (postgres or sqlite) is created and populated with anchor data. This also creates entries for the anchor_methods table (tells how the anchors were created). In this case, it is the methods anchor. For the trimmed anchors, Zack's data will have anchorid, chrom,trimmed_start, trimmed_end, left_trim_count, right_trim_count. Need to take this file and create a file that contains the formats: chrom, startPos, endPos, geneStart, GeneEnd

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
LoadGenomeIntervalsToPHGdbPlugin()
LoadGenomeIntervalsToPHGdbPlugin(Frame parentFrame)
LoadGenomeIntervalsToPHGdbPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	anchors() Tab-delimited file containing chrom, start position, end position
LoadGenomeIntervalsToPHGdbPlugin	anchors(String value) Set Anchors 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
LoadGenomeIntervalsToPHGdbPlugin	genomeData(String value) Set Genome Data File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
static void	main(String[] args)
void	postProcessParameters()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	refGenome() Referemce Genome File for aligning against
LoadGenomeIntervalsToPHGdbPlugin	refGenome(String value) Set Reference Genome File.

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

LoadGenomeIntervalsToPHGdbPlugin

public LoadGenomeIntervalsToPHGdbPlugin()

LoadGenomeIntervalsToPHGdbPlugin

public LoadGenomeIntervalsToPHGdbPlugin(Frame parentFrame)

LoadGenomeIntervalsToPHGdbPlugin

public LoadGenomeIntervalsToPHGdbPlugin(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

main

public static void main(String[] args)

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

refGenome

public String refGenome()

Referemce Genome File for aligning against

Returns:

Reference Genome File

refGenome

public LoadGenomeIntervalsToPHGdbPlugin refGenome(String value)

Set Reference Genome File. Referemce Genome File for aligning against

Parameters:

value - Reference Genome File

Returns:

this plugin

anchors

public String anchors()

Tab-delimited file containing chrom, start position, end position

Returns:

Anchors File

anchors

public LoadGenomeIntervalsToPHGdbPlugin anchors(String value)

Set Anchors File. Tab-delimited file containing chrom, start position, end position

Parameters:

value - Anchors 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 LoadGenomeIntervalsToPHGdbPlugin 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