net.maizegenetics.pangenome.db_loading

Class HaplotypeGeneMetricsPlugin

net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin

public class HaplotypeGeneMetricsPlugin

Class to analyse haplotype coverage of genes. Currently it takes a directory of files, one per genotype, that contain the list of ref range ids that appear in the haplotypes table for that genotype. This was created via the sql query: (first get list of gamete_grp_ids for each genotype), then for each gamete_grp_id do:

select haplotypes.ref_range_id from haplotypes INNER JOIN reference_ranges on reference_ranges.ref_range_id = haplotypes.ref_range_id INNER JOIN ref_range_ref_range_method on ref_range_ref_range_method.ref_range_id=reference_ranges.ref_range_id INNER JOIN methods on ref_range_ref_range_method.method_id = methods.method_id AND methods.name = 'refRegionGroup' and haplotypes.gamete_grp_id=3;

NOTE - the above query is no longer correct - it needs to use user-defined method names instead of refRegionGroup to get the files needed. But the code below that analyzes these files stands.

2 tests to be run: kotlin/db_loading/HaplotypeGEneMetricsPluginTest has testHaplotypeGeneMetricsPlugin createFastaForBlast One creates list of refRangeIds/genes in ref but not in each assembly, the other creates a blast file of specified ref range sequences.

The run blastdb (db created from assembly fasta) and blastn (fastas of selected reference sequences blasted against the assembly blast db) to see if these ranges exist in the assemblies but were missed by mummer4/nucmer.

Constructor Detail

HaplotypeGeneMetricsPlugin

public HaplotypeGeneMetricsPlugin(@Nullable
                                  java.awt.Frame parentFrame,
                                  boolean isInteractive)

Class to analyse haplotype coverage of genes. Currently it takes a directory of files, one per genotype, that contain the list of ref range ids that appear in the haplotypes table for that genotype. This was created via the sql query: (first get list of gamete_grp_ids for each genotype), then for each gamete_grp_id do:

select haplotypes.ref_range_id from haplotypes INNER JOIN reference_ranges on reference_ranges.ref_range_id = haplotypes.ref_range_id INNER JOIN ref_range_ref_range_method on ref_range_ref_range_method.ref_range_id=reference_ranges.ref_range_id INNER JOIN methods on ref_range_ref_range_method.method_id = methods.method_id AND methods.name = 'refRegionGroup' and haplotypes.gamete_grp_id=3;

NOTE - the above query is no longer correct - it needs to use user-defined method names instead of refRegionGroup to get the files needed. But the code below that analyzes these files stands.

2 tests to be run: kotlin/db_loading/HaplotypeGEneMetricsPluginTest has testHaplotypeGeneMetricsPlugin createFastaForBlast One creates list of refRangeIds/genes in ref but not in each assembly, the other creates a blast file of specified ref range sequences.

The run blastdb (db created from assembly fasta) and blastn (fastas of selected reference sequences blasted against the assembly blast db) to see if these ranges exist in the assemblies but were missed by mummer4/nucmer.

Method Detail

processData

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

getToolTipText

@NotNull
public java.lang.String getToolTipText()

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

inputDir

@NotNull
public java.lang.String inputDir()

Directory with files of haplotypes reference ranges

Returns:

Input Dir

inputDir

@NotNull
public HaplotypeGeneMetricsPlugin inputDir(@NotNull
                                                    java.lang.String value)

Set Input Dir. Directory with files of haplotypes reference ranges

Parameters:

value - Input Dir

Returns:

this plugin

refName

@NotNull
public java.lang.String refName()

Name of file containing reference genes

Returns:

Ref File Name

refName

@NotNull
public HaplotypeGeneMetricsPlugin refName(@NotNull
                                                   java.lang.String value)

Set Ref File Name. Name of file containing reference genes

Parameters:

value - Ref File Name

Returns:

this plugin

refRangeFile

@NotNull
public java.lang.String refRangeFile()

File containing reference range information: csv with columns ref_range_id, chrom,range_start,range_end

Returns:

Ref Range File

refRangeFile

@NotNull
public HaplotypeGeneMetricsPlugin refRangeFile(@NotNull
                                                        java.lang.String value)

Set Ref Range File. File containing reference range information: csv with columns ref_range_id, chrom,range_start,range_end

Parameters:

value - Ref Range File

Returns:

this plugin

outputFile

@NotNull
public java.lang.String outputFile()

File for writing matrix of gene coverage

Returns:

Output File

outputFile

@NotNull
public HaplotypeGeneMetricsPlugin outputFile(@NotNull
                                                      java.lang.String value)

Set Output File. File for writing matrix of gene coverage

Parameters:

value - Output File

Returns:

this plugin