net.maizegenetics.pangenome.hapCalling

Class ConvertRampSeqTagsToMapPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin

All Implemented Interfaces:

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

public class ConvertRampSeqTagsToMapPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Created by zrm22 on 10/4/17.

This plugin expects 2 input files as plugin parameters and a HaplotypeGraph object passed in as an input DataSet. It will output a Multimap where TaxonName is a String and the HaplotypeNodes are the nodes associated with tags which are found in those taxa

First file, hapIdMappingFile is a tab separated text file having the following format: Tag Node ChiSq L9.6366CA9D 12066644 55.9832 L9.95C33216 11966694 155.464 L9.2A55A52D 12278394 125.181 L9.99A622E8 11952178 421.905 L9.441428C4 12196601 169.546 There can be additional columns, but the first three need to be this way. It also helps if you prefilter the text file to only contain one Tag->Node mapping for each tag. In the test case we pick the best Node with the highest ChiSq for each tag to speed up processing

The Second file is a presence/absence matrix for each taxa we want to push through the pipeline. Also is tab separated text file in the form: TagID Tag A188 A239 L9.FE0EFC71 ACATCGAGCTTGGCCTGCATCTCGCGGATTTGCTCGAGCTGTGTGTCCTGACCCCCCGCAGGGACTGGGACCACAGCTAGCTCCAGCAGGATGTCAACGCGAGGCGCAGGCCCAAGGGGATCGTCATCCTC 0 0 L9.5DCFAAB9 ACGTCGAGCCTGGCCTACATCTCGCGGATTTGCTCGAGCTGTGCGTCCTGACCCCCCGTAGGGACTAGGAACATAGCTAGCTCCCGAAGGATGTCAACGCGAGGCACATGCCTAGGGGGATCACCGTCCTC 0 1 L9.188D3BB2 ACGTCGAGCCTGGCCTGTACCTCGCGAATTTGCTCGAGCTGTGCGTCCTGACCCCCCGCAGGGACTGGGACCACAGCTAGCTCCCGAAGGATGTCAACGCGAGGCGCAGGCCTAGGGGGATCACCGTCCTC 0 0

Where 1 means that taxa had a hit for that tag. This file can have as many columns as needed, but the first two are expected to be TagID and the Tag sequence.

The plugin will go through and add entries into the Multimap for each taxon->HapNode pair(Exactly the same as what is returned from HapCountBestPathToVCFPlugin). This Multimap is then used by the PathsToVCFPlugin to output a vcf file.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
ConvertRampSeqTagsToMapPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	pluginDescription()
String	pluginUserManualURL()
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input) Plugin method to process the data
String	tagCountsByTaxaFile() File holding the tag counts for each taxa
ConvertRampSeqTagsToMapPlugin	tagCountsByTaxaFile(String value) Set Tag Count By Taxa File.
String	tagToHapIdMapFile() tagToHapIDMappingFile
ConvertRampSeqTagsToMapPlugin	tagToHapIdMapFile(String value) Set Hap Id Mapping File.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, 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

ConvertRampSeqTagsToMapPlugin

public ConvertRampSeqTagsToMapPlugin(Frame parentFrame,
                                     boolean isInteractive)

Method Detail

processData

public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)

Plugin method to process the data

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

Parameters:

input - A DataSet Object where a HaplotypeGraph is the first element in the data structure

Returns:

Dataset with the TaxaNameToHaplotypeId multimap

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

pluginDescription

public String pluginDescription()

Specified by:

pluginDescription in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginDescription in class net.maizegenetics.plugindef.AbstractPlugin

pluginUserManualURL

public String pluginUserManualURL()

Specified by:

pluginUserManualURL in interface net.maizegenetics.plugindef.Plugin

Overrides:

pluginUserManualURL in class net.maizegenetics.plugindef.AbstractPlugin

tagToHapIdMapFile

public String tagToHapIdMapFile()

tagToHapIDMappingFile

Returns:

Hap Id Mapping File

tagToHapIdMapFile

public ConvertRampSeqTagsToMapPlugin tagToHapIdMapFile(String value)

Set Hap Id Mapping File. tagToHapIDMappingFile

Parameters:

value - Hap Id Mapping File

Returns:

this plugin

tagCountsByTaxaFile

public String tagCountsByTaxaFile()

File holding the tag counts for each taxa

Returns:

Tag Count By Taxa File

tagCountsByTaxaFile

public ConvertRampSeqTagsToMapPlugin tagCountsByTaxaFile(String value)

Set Tag Count By Taxa File. File holding the tag counts for each taxa

Parameters:

value - Tag Count By Taxa File

Returns:

this plugin