net.maizegenetics.pangenome.processAssemblyGenomes

Class AssemblyHaplotypesPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin

All Implemented Interfaces:

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

public class AssemblyHaplotypesPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Process Assemblies - both anchor and interanchor. This class exercises the following tools: mummer4 scripts: (nucmer, delta-filter, show-coords, show-snps) Algorithm: 1. run mummer4:nucmer with the parameters -c 250 --mum 2. run mummer4:show-coords with parameters -T -r (tab-delimited, sorted by ref) 3. run mummer4:show-snps with parameters -T -r (tab-delimited, sorted by ref ID and SNP positions) 4. Interanchors. a. Processed the same as the anchors. The VariantContext code grabs sequence aligning to both. We expect a certain linearity to the alignments. There will be large indels between sequences that are picked up as inter-genic regions. 5. The DB is loaded in batches of 3000 reference_ranges at a time. Assumptions/requirements: 1. alignments are on a per-chromosome basis: I expect fastas to be broken down by chromosome, 1 chrom per fasta 2. Id lines in fasta must start with >X, or >chrX or >chromosomeX where X is the chromosome number. Additional data is allowed after a space, but the first data must identify the chromosome as above. 3. The assembly and reference chromosomes need to be named in a similar fashion to allow for db matching of genome_interval_ids IE, if the ref chrom name has a number without leading 0's, so must the assembly. IE, chr1 for ref, then chr1 for assembly. 4. For populating the DB per Ed: ploidy=1, genes/chroms phased=TRUE (put the confidence at 1)

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
AssemblyHaplotypesPlugin()
AssemblyHaplotypesPlugin(Frame parentFrame)
AssemblyHaplotypesPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	assembly() Assembly fasta file for a single chromosome to align against the reference
AssemblyHaplotypesPlugin	assembly(String value) Set Assembly Fasta File.
String	assemblyName() Name of Assembly Taxon, to be stored as taxon name in the DB
AssemblyHaplotypesPlugin	assemblyName(String value) Set Assembly Name.
String	chrom() Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly
AssemblyHaplotypesPlugin	chrom(String value) Set Chromosome Name.
Integer	clusterSize() Cluster size to use with mummer4 nucmer script.
AssemblyHaplotypesPlugin	clusterSize(Integer value) Set Mummer4 Nucmer Cluster Size .
static Map<Integer,AnchorDataPHG>	createAndLoadAssemblyData(Map<Integer,ReferenceRange> idByRangeMap, List<htsjdk.variant.variantcontext.VariantContext> fullVC, net.maizegenetics.dna.map.GenomeSequence refSequence, Connection dbConn, String assemblyName, String outputDir, String chrom, int clusterSize) Create the assembly genotype/haplotype data and load to the PHG database
String	dbConfigFile() File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
AssemblyHaplotypesPlugin	dbConfigFile(String value) Set DB Config File.
static com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position>	getAnchorRangeSet(Map<Integer,ReferenceRange> anchorEntries) Create a RangeSet from a map of ranges
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	gVCFOutputDir() Directory for gvcf files to be output for later use
AssemblyHaplotypesPlugin	gVCFOutputDir(String value) Set GVCF Output Dir.
static void	loadAssemblyDataToDB(int gamete_grp_id, String method, Connection dbConn, Map<Integer,AnchorDataPHG> anchorSequences) Load the assembly haplotype data to the database
static int	loadInitialAssemblyData(String assemblyName, String method, Connection dbConn) load initial genotype and method data to the database
String	mummer4Path() Path to mummer4 binaries
AssemblyHaplotypesPlugin	mummer4Path(String value) Set Mummer4 binary path
String	outputDir() Output directory including trailing / for writing files
AssemblyHaplotypesPlugin	outputDir(String value) Set Output Directory.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	ref() Input reference fasta file for single chromosome
AssemblyHaplotypesPlugin	ref(String value) Set Reference Fasta File.
static Map<Integer,ReferenceRange>	referenceRangeForChromMap(Connection database, String chrom) Find all reference ranges for a particular chromosome

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

AssemblyHaplotypesPlugin

public AssemblyHaplotypesPlugin()

AssemblyHaplotypesPlugin

public AssemblyHaplotypesPlugin(Frame parentFrame)

AssemblyHaplotypesPlugin

public AssemblyHaplotypesPlugin(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

referenceRangeForChromMap

public static Map<Integer,ReferenceRange> referenceRangeForChromMap(Connection database,
                                                                    String chrom)

Find all reference ranges for a particular chromosome

Parameters:

database -

chrom -

Returns:

getAnchorRangeSet

public static com.google.common.collect.RangeSet<net.maizegenetics.dna.map.Position> getAnchorRangeSet(Map<Integer,ReferenceRange> anchorEntries)

Create a RangeSet from a map of ranges

Parameters:

anchorEntries -

Returns:

createAndLoadAssemblyData

public static Map<Integer,AnchorDataPHG> createAndLoadAssemblyData(Map<Integer,ReferenceRange> idByRangeMap,
                                                                   List<htsjdk.variant.variantcontext.VariantContext> fullVC,
                                                                   net.maizegenetics.dna.map.GenomeSequence refSequence,
                                                                   Connection dbConn,
                                                                   String assemblyName,
                                                                   String outputDir,
                                                                   String chrom,
                                                                   int clusterSize)

Create the assembly genotype/haplotype data and load to the PHG database

Parameters:

idByRangeMap -

fullVC -

refSequence -

dbConn -

assemblyName -

outputDir -

chrom -

Returns:

loadInitialAssemblyData

public static int loadInitialAssemblyData(String assemblyName,
                                          String method,
                                          Connection dbConn)

load initial genotype and method data to the database

Parameters:

assemblyName -

method -

dbConn -

Returns:

loadAssemblyDataToDB

public static void loadAssemblyDataToDB(int gamete_grp_id,
                                        String method,
                                        Connection dbConn,
                                        Map<Integer,AnchorDataPHG> anchorSequences)

Load the assembly haplotype data to the database

Parameters:

gamete_grp_id -

method -

dbConn -

anchorSequences -

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

ref

public String ref()

Input reference fasta file for single chromosome

Returns:

Reference Fasta File

ref

public AssemblyHaplotypesPlugin ref(String value)

Set Reference Fasta File. Input reference fasta file for single chromosome

Parameters:

value - Reference Fasta File

Returns:

this plugin

assembly

public String assembly()

Assembly fasta file for a single chromosome to align against the reference

Returns:

Assembly Fasta File

assembly

public AssemblyHaplotypesPlugin assembly(String value)

Set Assembly Fasta File. Assembly fasta file for a single chromosome to align against the reference

Parameters:

value - Assembly Fasta File

Returns:

this plugin

outputDir

public String outputDir()

Output directory including trailing / for writing files

Returns:

Output Directory

outputDir

public AssemblyHaplotypesPlugin outputDir(String value)

Set Output Directory. Output directory including trailing / for writing files

Parameters:

value - Output Directory

Returns:

this plugin

dbConfigFile

public String dbConfigFile()

File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection

Returns:

DB Config File

dbConfigFile

public AssemblyHaplotypesPlugin dbConfigFile(String value)

Set DB Config File. File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection

Parameters:

value - DB Config File

Returns:

this plugin

assemblyName

public String assemblyName()

Name of Assembly Taxon, to be stored as taxon name in the DB

Returns:

Assembly Name

assemblyName

public AssemblyHaplotypesPlugin assemblyName(String value)

Set Assembly Name. Name of Assembly Taxon, to be stored as taxon name in the DB

Parameters:

value - Assembly Name

Returns:

this plugin

chrom

public String chrom()

Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly

Returns:

Chromosome Name

chrom

public AssemblyHaplotypesPlugin chrom(String value)

Set Chromosome Name. Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly

Parameters:

value - Chromosome Name

Returns:

this plugin

mummer4Path

public String mummer4Path()

Path to mummer4 binaries

Returns:

Path to mummer 4 binaries

mummer4Path

public AssemblyHaplotypesPlugin mummer4Path(String value)

Set Mummer4 binary path

Parameters:

value - Mummer4 binary path

Returns:

this plugin

clusterSize

public Integer clusterSize()

Cluster size to use with mummer4 nucmer script.

Returns:

Mummer4 Nucmer Cluster Size

clusterSize

public AssemblyHaplotypesPlugin clusterSize(Integer value)

Set Mummer4 Nucmer Cluster Size . Cluster size to use with mummer4 nucmer script.

Parameters:

value - Mummer4 Nucmer Cluster Size

Returns:

this plugin

gVCFOutputDir

public String gVCFOutputDir()

Directory for gvcf files to be output for later use

Returns:

GVCF Output Dir

gVCFOutputDir

public AssemblyHaplotypesPlugin gVCFOutputDir(String value)

Set GVCF Output Dir. Directory for gvcf files to be output for later use

Parameters:

value - GVCF Output Dir

Returns:

this plugin