net.maizegenetics.pangenome.pipelineTests

Class CountNsInRawHapSequencesPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin

All Implemented Interfaces:

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

public class CountNsInRawHapSequencesPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Calculates the percentage of N's for each "raw" haplotype (ie, not consensus) for each genome interval (anchor, not inter-anchors). Results shoudl be printed to a tab-delimited file with genome_interval_id as rows, and taxa/percentage as the columns. Testing: Testing was done by random manual checking. Once the output file is created, it is uploaded to excel. use sqlite3 on machine holding db. Look at sequences and verify when it has "1" as percent, there are all N's. WHen 0, there are 0. When a percentage, e.g. .53, the sequence looks to be half N's. Find gamete_grp_id for the line you want to check: sqlite> SELECT gamete_haplotypes.gamete_grp_id FROM gamete_haplotypes sqlite> INNER JOIN gametes ON gametes.gameteid=gamete_haplotypes.gameteid sqlite> INNER JOIN genotypes on gametes.genoid=genotypes.genoid sqlite> WHERE genotypes.line_name='CML247'; sqlite> 5 (this is returned value) Then look at the sequence: sqlite> select gamete_grp_id, genome_interval_id,sequence from haplotypes where gamete_grp_id=5 and genome_interval_id=111;

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
CountNsInRawHapSequencesPlugin()
CountNsInRawHapSequencesPlugin(Frame parentFrame)
CountNsInRawHapSequencesPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	databaseName() Database name
CountNsInRawHapSequencesPlugin	databaseName(String value) Set Database Name.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	hostname() Hostname where database resides
CountNsInRawHapSequencesPlugin	hostname(String value) Set Hostname.
static void	main(String[] args)
String	outputFile() Output File
CountNsInRawHapSequencesPlugin	outputFile(String value) Set Output File.
String	password() Password for database
CountNsInRawHapSequencesPlugin	password(String value) Set Password.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	userid() Userid for database
CountNsInRawHapSequencesPlugin	userid(String value) Set Userid.

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

CountNsInRawHapSequencesPlugin

public CountNsInRawHapSequencesPlugin()

CountNsInRawHapSequencesPlugin

public CountNsInRawHapSequencesPlugin(Frame parentFrame)

CountNsInRawHapSequencesPlugin

public CountNsInRawHapSequencesPlugin(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

main

public static void main(String[] args)

Parameters:

args -

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

hostname

public String hostname()

Hostname where database resides

Returns:

Hostname

hostname

public CountNsInRawHapSequencesPlugin hostname(String value)

Set Hostname. Hostname where database resides

Parameters:

value - Hostname

Returns:

this plugin

userid

public String userid()

Userid for database

Returns:

Userid

userid

public CountNsInRawHapSequencesPlugin userid(String value)

Set Userid. Userid for database

Parameters:

value - Userid

Returns:

this plugin

password

public String password()

Password for database

Returns:

Password

password

public CountNsInRawHapSequencesPlugin password(String value)

Set Password. Password for database

Parameters:

value - Password

Returns:

this plugin

databaseName

public String databaseName()

Database name

Returns:

Database Name

databaseName

public CountNsInRawHapSequencesPlugin databaseName(String value)

Set Database Name. Database name

Parameters:

value - Database Name

Returns:

this plugin

outputFile

public String outputFile()

Output File

Returns:

Output File

outputFile

public CountNsInRawHapSequencesPlugin outputFile(String value)

Set Output File. Output File

Parameters:

value - Output File

Returns:

this plugin