CreateIntervalsFileFromGffPlugin (net.maizegenetics:phg 0.0.1 API)

java.lang.Object
- net.maizegenetics.plugindef.AbstractPlugin
- - net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener
```
public class CreateIntervalsFileFromGffPlugin
extends net.maizegenetics.plugindef.AbstractPlugin
```
This class creates the interval files needed for running GATK haplotype caller, and the csv files needed for loading reference sequence into the database. Two sets of files are created: one set has coordinates based just on the ref gene coordinates. The other is gene coordinates plus user-specified flanking regions Algorithm: 1. read gff file, grab gene coordinates 2. For each Chromosome: merge genes that overlap, toss genes that are embedded within another gene Store list as mergedGeneList. 3. Using the mergedGeneList in 3, create 2nd per-chrom coordinate lists that includes flanking regions 4. Write files: interval format (chrom:start-end): a. mergedGeneList; b. mergedGEneList with flanking csv format (chr,anchorstart,anchorend,geneStart,geneEnd,geneName) a. mergedGeneList; b. mergedGEneList with flanking debug files: List of merged, list of embedded files written for informational purposes NOTE: the csv files contain the name of all genes contained in an anchor. This data is not stored in the DB. IT is included because the biologists have at times asked for it and this is a good place for it to be stored and retrieved. INPUT: 1. refFile: String: path to reference genome. needed to find size of chromosomes for adding flanking regions to last chrom entry. 2. geneFile: String: path to single file containing all chrom gene data in GFF format; or path to directory containing per-chrom files with gene data in GFF format. These data files must consist of GFF gene data alone, not the full gff. 3. outputBase: String: directory, including trailing "/", where output files will be written. 4. numFlanking: int: number of flanking bps to add on each end of the anchors. OUTPUT: 1. intervals file based on gene coordinates. 2. intervals file based on gene coordinates + numflanking bps 3. csv file based on gene coordinates 4. csv file based on gene coordinates + numflanking bps

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
`CreateIntervalsFileFromGffPlugin()`
`CreateIntervalsFileFromGffPlugin(Frame parentFrame)`
`CreateIntervalsFileFromGffPlugin(Frame parentFrame, boolean isInteractive)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`geneFile()` Tab delimited .txt file containing gene-only GFF data from reference GFF file,
`CreateIntervalsFileFromGffPlugin`	`geneFile(String value)` Set Gene File.
`String`	`getButtonName()`
`ImageIcon`	`getIcon()`
`String`	`getToolTipText()`
`Integer`	`numFlanking()` Number of flanking basepairs to add at each end of the gene sequence
`CreateIntervalsFileFromGffPlugin`	`numFlanking(Integer value)` Set Number of Flanking BPs.
`String`	`outputDir()` Directory where output files will be written
`CreateIntervalsFileFromGffPlugin`	`outputDir(String value)` Set Output Directory.
`net.maizegenetics.plugindef.DataSet`	`processData(net.maizegenetics.plugindef.DataSet input)`
`String`	`refFile()` Fasta file containing reference genome
`CreateIntervalsFileFromGffPlugin`	`refFile(String value)` Set Ref Genome File.
`String`	`runPlugin(net.maizegenetics.plugindef.DataSet input)` Convenience method to run plugin with one return object.

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
  - CreateIntervalsFileFromGffPlugin
```
public CreateIntervalsFileFromGffPlugin()
```
  - CreateIntervalsFileFromGffPlugin
```
public CreateIntervalsFileFromGffPlugin(Frame parentFrame)
```
  - CreateIntervalsFileFromGffPlugin
```
public CreateIntervalsFileFromGffPlugin(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
  - runPlugin
```
public String runPlugin(net.maizegenetics.plugindef.DataSet input)
```
    Convenience method to run plugin with one return object.
  - getIcon
```
public ImageIcon getIcon()
```
  - getButtonName
```
public String getButtonName()
```
  - getToolTipText
```
public String getToolTipText()
```
  - refFile
```
public String refFile()
```
    Fasta file containing reference genome
    
    Returns:
    
    Ref Genome File
  - refFile
```
public CreateIntervalsFileFromGffPlugin refFile(String value)
```
    Set Ref Genome File. Fasta file containing reference genome
    
    Parameters:
    
    value - Ref Genome File
    
    Returns:
    
    this plugin
  - geneFile
```
public String geneFile()
```
    Tab delimited .txt file containing gene-only GFF data from reference GFF file,
    
    Returns:
    
    Gene File
  - geneFile
```
public CreateIntervalsFileFromGffPlugin geneFile(String value)
```
    Set Gene File. Tab delimited .txt file containing gene-only GFF data from reference GFF file,
    
    Parameters:
    
    value - Gene File
    
    Returns:
    
    this plugin
  - outputDir
```
public String outputDir()
```
    Directory where output files will be written
    
    Returns:
    
    Output Directory
  - outputDir
```
public CreateIntervalsFileFromGffPlugin outputDir(String value)
```
    Set Output Directory. Directory where output files will be written
    
    Parameters:
    
    value - Output Directory
    
    Returns:
    
    this plugin
  - numFlanking
```
public Integer numFlanking()
```
    Number of flanking basepairs to add at each end of the gene sequence
    
    Returns:
    
    Number of Flanking BPs
  - numFlanking
```
public CreateIntervalsFileFromGffPlugin numFlanking(Integer value)
```
    Set Number of Flanking BPs. Number of flanking basepairs to add at each end of the gene sequence
    
    Parameters:
    
    value - Number of Flanking BPs
    
    Returns:
    
    this plugin

Class CreateIntervalsFileFromGffPlugin

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

Constructor Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class java.lang.Object

Methods inherited from interface net.maizegenetics.plugindef.Plugin

Constructor Detail

CreateIntervalsFileFromGffPlugin

CreateIntervalsFileFromGffPlugin

CreateIntervalsFileFromGffPlugin

Method Detail

processData

runPlugin

getIcon

getButtonName

getToolTipText

refFile

refFile

geneFile

geneFile

outputDir

outputDir

numFlanking

numFlanking