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/*
* MergeRenameDeleteTaxaPlugin
*/
package net.maizegenetics.analysis.data;
import net.maizegenetics.dna.snp.GenotypeTable;
import net.maizegenetics.dna.snp.GenotypeTableBuilder;
import net.maizegenetics.dna.snp.NucleotideAlignmentConstants;
import net.maizegenetics.dna.snp.genotypecall.BasicGenotypeMergeRule;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.plugindef.Datum;
import net.maizegenetics.plugindef.PluginParameter;
import net.maizegenetics.taxa.TaxaList;
import net.maizegenetics.taxa.Taxon;
import net.maizegenetics.util.GeneralAnnotation;
import net.maizegenetics.util.Utils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import javax.swing.*;
import java.awt.*;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.List;
/**
* @author jcg233
*/
public class MergeRenameDeleteTaxaPlugin extends net.maizegenetics.plugindef.AbstractPlugin {
@Override
public String pluginDescription() {
return "Rename taxa, merging those with the same new name in the taxa rename key file. "
+ "Taxa with the new name \"delete\" will be removed.";
}
private PluginParameter taxaRenameKey = new PluginParameter.Builder<>("renameKey", null, String.class)
.required(true)
.inFile()
.guiName("Taxa Rename Key")
.description("Tab-delimited file with original and new taxa names. Taxa with the same new name will be merged. "
+ "Taxa with the new name \"delete\" will be removed. Any other columns (and the header line) are ignored.")
.build();
private PluginParameter outputHDF5Genotypes = new PluginParameter.Builder<>("o", null, String.class)
.guiName("Output HDF Genotypes")
.required(true)
.outFile()
.description("Output HDF5 genotypes file").build();
private PluginParameter avgSeqErrorRate = new PluginParameter.Builder<>("eR", 0.01, Double.class)
.guiName("Avg Seq Error Rate")
.description("Average sequencing error rate per base (used to decide between heterozygous and homozygous calls when merging taxa)")
.build();
private PluginParameter noDepthOutput = new PluginParameter.Builder<>("ndo", false, Boolean.class)
.guiName("No Depth Output")
.description("No depth output: do not write depths to the output HDF5 genotypes file")
.build();
private PluginParameter dataSetName = new PluginParameter.Builder<>("name", null, String.class)
.guiName("Data set name")
.required(false)
.description("(Optional) Short data set name to be added as an root level annotation under \"dataSetName\"")
.build();
private PluginParameter dataSetDescription = new PluginParameter.Builder<>("desc", null, String.class)
.guiName("Data set description")
.required(false)
.description("(Optional) Short data set description to be added as an root level annotation under \"dataSetDescription\"")
.build();
public MergeRenameDeleteTaxaPlugin() {
super(null, false);
}
public MergeRenameDeleteTaxaPlugin(Frame parentFrame, boolean isInteractive) {
super(parentFrame, isInteractive);
}
private static final Logger myLogger = LogManager.getLogger(MergeRenameDeleteTaxaPlugin.class);
String dataSetDescrip, date;
String errorMessage;
private GenotypeTable inputGenotypes = null;
private String inputGenosName = null;
private TreeMap> newNameToOldNames = new TreeMap();
private BasicGenotypeMergeRule genoMergeRule = null;
private GenotypeTableBuilder genos = null; //output genotype table
private TaxaList taxaList = null;
@Override
protected void preProcessParameters(DataSet input) {
if (input == null) {
throw new IllegalArgumentException("MergeRenameDeleteTaxaPlugin: preProcessParameters: Please select one Genotype Table.");
}
List genotypeTables = input.getDataOfType(GenotypeTable.class);
inputGenosName = genotypeTables.get(0).getName();
myLogger.info("\n" + pluginDescription() + "\n");
myLogger.info("Input genotype name: " + inputGenosName);
if (genotypeTables.size() == 1) {
inputGenotypes
= (GenotypeTable) genotypeTables.get(0).getData();
taxaList = inputGenotypes.taxa();
} else {
throw new IllegalArgumentException("MergeRenameDeleteTaxaPlugin: preProcessParameters: Please select one Genotype Table.");
}
date = new SimpleDateFormat("yyyyMMdd").format(new Date());
String outfile = outputHDF5Genotypes();
outputHDF5Genotypes(outfile.replace("__DATE__", "_" + date));
}
public DataSet processData(DataSet input) {
readTaxaRenameKey();
setUpHDF5GenotypeTableBuilder();
int nTaxaAdded = addRenamedMergedTaxa();
if (dataSetName() != null) {
genos.dataSetName(parseDataSetName(dataSetName()));
}
if (dataSetDescription() != null) {
genos.dataSetDescription(parseDataSetDescription(dataSetDescription(), nTaxaAdded));
}
genos.build();
myLogger.info("\n\nFinished creating new HDF5 genotpye file with merged and renamed taxa.\n\n");
return null;
}
private void readTaxaRenameKey() {
myLogger.info("\nReading the taxaRenameKey file:\n " + taxaRenameKey() + "\n");
BufferedReader taxaRenameKeyReader = Utils.getBufferedReader(taxaRenameKey());
String line;
int nLinesRead = 0;
try {
while ((line = taxaRenameKeyReader.readLine()) != null) {
nLinesRead++;
if (nLinesRead == 1) {
continue; // skip the header
}
String[] values = line.split("\t", -1);
String oldName = values[0];
String newName = values[1];
if (!newNameToOldNames.containsKey(newName)) {
newNameToOldNames.put(newName, new TreeSet());
}
newNameToOldNames.get(newName).add(oldName);
}
} catch (IOException e) {
System.err.println("\n\nProblem reading the taxaRenameKey file (" + taxaRenameKey() + "):\n\t" + e);
System.exit(1);
}
myLogger.info("\nFinished reading the taxaRenameKey file (nTaxa=" + (nLinesRead - 1) + ")\n");
}
private void setUpHDF5GenotypeTableBuilder() {
genoMergeRule = new BasicGenotypeMergeRule(avgSeqErrorRate());
File hdf5File = new File(outputHDF5Genotypes());
if (hdf5File.exists()) {
errorMessage = "\nERROR: the output HDF5 genotypes file:\n " + outputHDF5Genotypes() + "\n already exists\n\n";
myLogger.error(errorMessage);
throw new IllegalStateException(errorMessage);
} else {
myLogger.info("\nInitializing the output HDF5 file:\n " + outputHDF5Genotypes() + "\n\n");
genos = GenotypeTableBuilder.getTaxaIncrementalWithMerging(outputHDF5Genotypes(), inputGenotypes.positions(), genoMergeRule);
}
}
private int addRenamedMergedTaxa() {
int nTaxaAdded = 0;
int nTaxaDeleted = 0;
for (Map.Entry> newNameAndOldNames : newNameToOldNames.entrySet()) {
String newName = newNameAndOldNames.getKey();
int nTaxaToMergeOrDelete = newNameAndOldNames.getValue().size();
if (newName.equals("delete") || newName.equals("remove")) {
nTaxaDeleted += nTaxaToMergeOrDelete;
continue;
}
StringBuilder oldNames = new StringBuilder();
Taxon.Builder TaxonBuilder = null;
int[][] alleleDepths = new int[NucleotideAlignmentConstants.NUMBER_NUCLEOTIDE_ALLELES][inputGenotypes.positions().numberOfSites()];
byte[] taxonGenos = null;
for (String oldName : newNameAndOldNames.getValue()) {
oldNames.append(oldName + ",");
Taxon oldTaxon = taxaList.get(taxaList.indexOf(oldName));
if (TaxonBuilder == null) {
TaxonBuilder = new Taxon.Builder(oldTaxon); // adds all the annotations from the first oldName taxon
TaxonBuilder = TaxonBuilder.name(newName);
} else {
GeneralAnnotation oldAnnos = oldTaxon.getAnnotation();
for (Map.Entry oldAnno : oldAnnos.getAllAnnotationEntries()) {
TaxonBuilder = TaxonBuilder.addAnno(oldAnno.getKey(), oldAnno.getValue());
}
}
TaxonBuilder = TaxonBuilder.addAnno("OldName", oldName);
if (inputGenotypes.hasDepth()) {
for (int site = 0; site < inputGenotypes.positions().numberOfSites(); site++) {
int[] alleleDepthsAtSite = inputGenotypes.depthForAlleles(taxaList.indexOf(oldName), site);
for (int allele = 0; allele < NucleotideAlignmentConstants.NUMBER_NUCLEOTIDE_ALLELES; allele++) {
alleleDepths[allele][site] += alleleDepthsAtSite[allele];
}
}
}
if (nTaxaToMergeOrDelete == 1) {
taxonGenos = inputGenotypes.genotypeAllSites(taxaList.indexOf(oldName));
}
}
if (nTaxaToMergeOrDelete > 1) {
if (inputGenotypes.hasDepth()) {
taxonGenos = resolveGenosForTaxon(alleleDepths);
} else {
throw new IllegalStateException("\n\nERROR: Merging genotypes across replicate taxa is not allowed when there is no depth\n\n");
}
}
if (noDepthOutput()) {
genos.addTaxon(TaxonBuilder.build(), taxonGenos, null);
} else {
genos.addTaxon(TaxonBuilder.build(), alleleDepths, taxonGenos);
}
myLogger.info(" ...finished calling/adding genotypes for " + newName + " OldName(s):" + oldNames.deleteCharAt(oldNames.length() - 1).toString());
nTaxaAdded++;
}
myLogger.info("\nFinished adding genotypes for " + nTaxaAdded + " taxa. nTaxaDeleted=" + nTaxaDeleted);
return nTaxaAdded;
}
private byte[] resolveGenosForTaxon(int[][] depthsForTaxon) {
int nAlleles = depthsForTaxon.length;
int[] depthsAtSite = new int[nAlleles];
int nSites = depthsForTaxon[0].length;
byte[] genos = new byte[nSites];
for (int site = 0; site < nSites; site++) {
for (int allele = 0; allele < nAlleles; allele++) {
depthsAtSite[allele] = depthsForTaxon[allele][site];
}
genos[site] = genoMergeRule.callBasedOnDepth(depthsAtSite);
}
return genos;
}
private String parseDataSetName(String dataSetName) {
return dataSetName.replace("__DATE__", "_" + date);
}
private String parseDataSetDescription(String dataSetDescrip, int nTaxa) {
int nSNPs = inputGenotypes.numberOfSites();
return dataSetDescrip.replace("__SNPS__", "" + nSNPs).replace("__TAXA__", "" + nTaxa).replace("__DATE__", date);
}
@Override
public ImageIcon getIcon() {
URL imageURL = MergeRenameDeleteTaxaPlugin.class
.getResource("/net/maizegenetics/analysis/images/lowDepthToMissing.gif");
if (imageURL == null) {
return null;
} else {
return new ImageIcon(imageURL);
}
}
@Override
public String getButtonName() {
return "MergeRenameTaxa";
}
@Override
public String getToolTipText() {
return "Rename taxa, merging those with the same new name";
}
/**
* Convenience method to run plugin with input and output GenotypeTable objects
* (rather than DataSets)
*
* @param inputGenos Input GenotypeTable.
*
* @return GenotypeTable where genotypes with depth below the specified minimum are set to missing.
*/
public void runPlugin(GenotypeTable inputGenos) {
DataSet input = new DataSet(new Datum("inputGenotypes", inputGenos, null), null);
runPlugin(input);
}
/**
* Convenience method to run plugin.
*/
public void runPlugin(DataSet input) {
performFunction(input);
}
/**
* Tab-delimited file with original and new taxa names.
* Taxa with the same new name will be merged. Taxa with
* the new name "delete" will be removed. Any other columns
* (and the header line) are ignored.
*
* @return Taxa Rename Key
*/
public String taxaRenameKey() {
return taxaRenameKey.value();
}
/**
* Set Taxa Rename Key. Tab-delimited file with original
* and new taxa names. Taxa with the same new name will
* be merged. Taxa with the new name "delete" will be
* removed. Any other columns (and the header line) are
* ignored.
*
* @param value Taxa Rename Key
*
* @return this plugin
*/
public MergeRenameDeleteTaxaPlugin taxaRenameKey(String value) {
taxaRenameKey = new PluginParameter<>(taxaRenameKey, value);
return this;
}
/**
* Output genotypes file
*
* @return Output Genotypes
*/
public String outputHDF5Genotypes() {
return outputHDF5Genotypes.value();
}
/**
* Set Output Genotypes. Output genotypes file
*
* @param value Output Genotypes
*
* @return this plugin
*/
public MergeRenameDeleteTaxaPlugin outputHDF5Genotypes(String value) {
outputHDF5Genotypes = new PluginParameter<>(outputHDF5Genotypes, value);
return this;
}
/**
* Average sequencing error rate per base (used to decide
* between heterozygous and homozygous calls when merging
* taxa)
*
* @return Avg Seq Error Rate
*/
public Double avgSeqErrorRate() {
return avgSeqErrorRate.value();
}
/**
* Set Avg Seq Error Rate. Average sequencing error rate
* per base (used to decide between heterozygous and homozygous
* calls when merging taxa)
*
* @param value Avg Seq Error Rate
*
* @return this plugin
*/
public MergeRenameDeleteTaxaPlugin avgSeqErrorRate(Double value) {
avgSeqErrorRate = new PluginParameter<>(avgSeqErrorRate, value);
return this;
}
/**
* No depth output: do not write depths to the output
* genotypes file (applies only to hdf5 or VCF)
*
* @return No Depth Output
*/
public Boolean noDepthOutput() {
return noDepthOutput.value();
}
/**
* Set No Depth Output. No depth output: do not write
* depths to the output genotypes file (applies only to
* hdf5 or VCF)
*
* @param value No Depth Output
*
* @return this plugin
*/
public MergeRenameDeleteTaxaPlugin noDepthOutput(Boolean value) {
noDepthOutput = new PluginParameter<>(noDepthOutput, value);
return this;
}
/**
* (Optional) Short data set name to be added as an root
* level annotation under "/DataSetName"
*
* @return Data set name
*/
public String dataSetName() {
return dataSetName.value();
}
/**
* Set Data set name. (Optional) Short data set name to
* be added as an root level annotation under "dataSetName"
*
* @param value Data set name
*
* @return this plugin
*/
public MergeRenameDeleteTaxaPlugin dataSetName(String value) {
dataSetName = new PluginParameter<>(dataSetName, value);
return this;
}
/**
* (Optional) Short data set description to be added as
* an root level annotation under "dataSetDescription"
*
* @return Data set description
*/
public String dataSetDescription() {
return dataSetDescription.value();
}
/**
* Set Data set description. (Optional) Short data set
* description to be added as an root level annotation
* under "/DataSetDescription"
*
* @param value Data set description
*
* @return this plugin
*/
public MergeRenameDeleteTaxaPlugin dataSetDescription(String value) {
dataSetDescription = new PluginParameter<>(dataSetDescription, value);
return this;
}
}
