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/**
*
*/
package net.maizegenetics.analysis.data;
import java.awt.Frame;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import javax.swing.ImageIcon;
import net.maizegenetics.dna.snp.GenotypeTable;
import net.maizegenetics.dna.snp.GenotypeTableUtils;
import net.maizegenetics.dna.snp.NucleotideAlignmentConstants;
import net.maizegenetics.plugindef.AbstractPlugin;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.plugindef.Datum;
import net.maizegenetics.plugindef.PluginParameter;
import net.maizegenetics.util.Utils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
/**
* Plugin to convert genotypes to parental comparisons and store them in an
* output file. The user can get outputs as A/H/B, 0/1/2, or 0/0.5/1 for a
* genotype matching parent A's genotype, heterozygous, or parent B's genotype
* respectively. If the genotype is neither A or B or a het combination of A/B
* (B/A) then it is coded as "NA".
*
* @author Stefan Reuscher
* @author jeff Glaubitz
* @author lynn Johnson
* @author Josh Guy
*
*/
public class GenosToABHPlugin extends AbstractPlugin {
private static final Logger myLogger = LogManager.getLogger(GenosToABHPlugin.class);
private ArrayList parentAIndices = null;
private ArrayList parentBIndices = null;
public static enum OUTPUT_CHECK {
c, i, r
}
private PluginParameter outfile = new PluginParameter.Builder<>("o", null, String.class)
.required(true).outFile().guiName("Output file").description("Output genotype file").build();
private PluginParameter parentA = new PluginParameter.Builder<>("parentA", null, String.class)
.required(true).guiName("Parent A").inFile()
.description("The full name of file containing list of taxa names for parent A").build();
private PluginParameter parentB = new PluginParameter.Builder<>("parentB", null, String.class)
.required(true).guiName("Parent B").inFile()
.description("The full name of file containing list of taxa names for parent B").build();
private PluginParameter outputFormat = new PluginParameter.Builder<>("outputFormat", OUTPUT_CHECK.c, OUTPUT_CHECK.class)
.required(false).guiName("Output Format")
.description("Enter \"c\" for A,H,B to code for parent A, het, and parent B; Enter \"i\" for 0, 1, 2 to code for parent A, het, and parent B; Enter \"r\" for 0, 0.5, 1 to code for parent A, het, and parent B")
.range(OUTPUT_CHECK.values()).build();
private GenotypeTable myInput = null;
public GenosToABHPlugin() {
super(null, false);
}
public GenosToABHPlugin(Frame parentFrame, boolean isInteractive) {
super(parentFrame, isInteractive);
}
@Override
protected void preProcessParameters(DataSet input) {
if (input == null) {
throw new IllegalArgumentException("GenosToABHPlugin: preProcessParameters: Please select one Genotype Table.");
}
List genotypeTables = input.getDataOfType(GenotypeTable.class);
if (genotypeTables.size() == 1) {
myInput = (GenotypeTable) genotypeTables.get(0).getData();
} else {
throw new IllegalArgumentException("GenosToABHPlugin: preProcessParameters: Please select one Genotype Table.");
}
}
/**
* The main method. Plugin to convert genotypes to parental comparisons and
* store them in an output file. The user can get outputs as A/H/B, 0/1/2,
* or 0/0.5/1 for a genotype matching parent A's genotype, heterozygous, or
* parent B's genotype respectively. If the genotype is neither A or B or a
* het combination of A/B (B/A) then it is coded as "NA".
*/
@Override
public DataSet processData(DataSet input) {
parentAIndices = getParentIndex(myInput, parentA());
parentBIndices = getParentIndex(myInput, parentB());
if (parentAIndices == null || parentAIndices.size() == 0 || parentBIndices == null
|| parentBIndices.size() == 0) {
return null;
}
byte[] parentAGenos = new byte[myInput.numberOfSites()];
byte[] parentBGenos = new byte[myInput.numberOfSites()];
byte[][] hets = new byte[2][myInput.numberOfSites()];
createParentalByteGenos(myInput, parentAGenos, parentBGenos, hets);
myLogger.info(String.format("GenosToABHPlugin: number Of sites:%d number of taxa:%d %n", myInput.numberOfSites(), myInput.numberOfTaxa()));
// Write converted genotypes to a text file
writeConvertedGenos(myInput, parentAGenos, parentBGenos, hets);
return null;
}
// Assumes a file format that contains NO header line. Each line
// contains one parental taxon name.
private ArrayList getParentIndex(GenotypeTable genos, String parentFile) {
try (BufferedReader reader = Utils.getBufferedReader(parentFile)) {
ArrayList parentNames = new ArrayList();
String line;
// Read each line of the parentFile, add the parent taxon
// to the ArrayList of parent names
while ((line = reader.readLine()) != null) {
parentNames.add(line);
}
// if there are parentNames, find their index in the genotype table
if (parentNames.size() > 0) {
ArrayList parentIndices = new ArrayList();
for (String parent : parentNames) {
int index = genos.taxa().indexOf(parent);
if (index >= 0) {
parentIndices.add(index);
} else {
myLogger.error("Parent " + parent + " missing from the genotype file");
return null;
}
}
System.out.println("File " + parentFile + " has " + parentIndices.size() + " elements");
return parentIndices;
} else {
myLogger.error("No parent names found in file: " + parentFile);
}
} catch (IOException exc) {
exc.printStackTrace();
}
return null;
}
// Create byte arrays to hold consensus parental genotypes
// Rejected sites will have parentAGenos[site] set to N (don't output these to converted ABH genotype file)
// Also create a 2-D byte array holding the corresponding heterozygous call for each site (in both possible phases)
public void createParentalByteGenos(GenotypeTable genos, byte[] parentAGenos, byte[] parentBGenos, byte[][] hets) {
int numAccepted = 0;
int numRejected = 0;
// Populate arrays with genotypes
for (int site = 0; site < genos.numberOfSites(); site++) {
// StringBuilder for output of parental genotypes of accepted and rejected sites to log
StringBuilder strB = new StringBuilder(genos.siteName(site));
// Resolve consensus genotypes for parents A and B
byte parentAGeno = getParentalGenotype(genos, parentAIndices, site);
byte parentBGeno = getParentalGenotype(genos, parentBIndices, site);
// reject sites that are not polymorphic or unknown or heterozygous in either parent
if (parentAGeno == parentBGeno
|| parentAGeno == GenotypeTable.UNKNOWN_DIPLOID_ALLELE
|| parentBGeno == GenotypeTable.UNKNOWN_DIPLOID_ALLELE
|| GenotypeTableUtils.isHeterozygous(parentAGeno)
|| GenotypeTableUtils.isHeterozygous(parentBGeno)) {
// reject
parentAGenos[site] = GenotypeTable.UNKNOWN_DIPLOID_ALLELE;
numRejected++;
strB.append("\treject");
} else {
// accept
parentAGenos[site] = parentAGeno;
parentBGenos[site] = parentBGeno;
// Takes the consensus parental genotypes and gives us the 2 possible heterozygotes
hets[0][site] = GenotypeTableUtils.getDiploidValuePhased(parentAGeno, parentBGeno);
hets[1][site] = GenotypeTableUtils.getDiploidValuePhased(parentBGeno, parentAGeno);
strB.append("\taccept");
numAccepted++;
}
strB.append("\t" + NucleotideAlignmentConstants.getNucleotideIUPAC(parentAGeno) + ":");
for (Integer parentAIdx : parentAIndices) {
strB.append(genos.genotypeAsString(parentAIdx, site));
}
strB.append("\t" + NucleotideAlignmentConstants.getNucleotideIUPAC(parentBGeno) + ":");
for (Integer parentBIdx : parentBIndices) {
strB.append(genos.genotypeAsString(parentBIdx, site));
}
myLogger.info(strB.toString());
}
myLogger.info("Number of accepted sites: " + numAccepted + ", number of Rejected sites: " + numRejected);
}
public byte getParentalGenotype(GenotypeTable genos, ArrayList parentIndices, int site) {
boolean finalIsUnknown = false;
byte finalParent = genos.genotype(parentIndices.get(0), site);
if (finalParent == GenotypeTable.UNKNOWN_DIPLOID_ALLELE) {
finalIsUnknown = true;
}
for (int idx = 1; idx < parentIndices.size(); idx++) {
byte nextGeno = genos.genotype(parentIndices.get(idx), site);
if (nextGeno != finalParent) {
if (finalIsUnknown) {
finalParent = nextGeno;
finalIsUnknown = false;
} else if (nextGeno != GenotypeTable.UNKNOWN_DIPLOID_ALLELE) {
// Mismatch - what do we set it to?
finalParent = GenotypeTable.UNKNOWN_DIPLOID_ALLELE;
return finalParent;
}
}
}
return finalParent;
}
private void writeConvertedGenos(GenotypeTable genos, byte[] parentAGenos, byte[] parentBGenos, byte[][] hets) {
try (BufferedWriter bw = Utils.getBufferedWriter(outfile())) {
// create the first line of the file - this is the header line,
// it contains the site names. Skip all sites where parentAGenos of
// that site == UNKNOWN_DIPLOID_ALLELE
StringBuilder strB = new StringBuilder("id");
for (int site = 0; site < genos.numberOfSites(); site++) {
if (parentAGenos[site] == GenotypeTable.UNKNOWN_DIPLOID_ALLELE) {
continue;
}
strB.append("," + genos.siteName(site));
}
writeLine(strB, bw); // writeline appends the newline
// Second line contains the chromosome names
strB = new StringBuilder("NA");
for (int site = 0; site < genos.numberOfSites(); site++) {
if (parentAGenos[site] == GenotypeTable.UNKNOWN_DIPLOID_ALLELE) {
continue;
}
strB.append("," + genos.chromosomeName(site));
}
writeLine(strB, bw);
// write the converted genotype for each taxon/site
for (int taxon = 0; taxon < genos.numberOfTaxa(); taxon++) {
if (parentAIndices.contains(taxon) || parentBIndices.contains(taxon)) {
continue; // skip the parents
}
strB = new StringBuilder(genos.taxaName(taxon));
for (int site = 0; site < genos.numberOfSites(); site++) {
if (parentAGenos[site] == GenotypeTable.UNKNOWN_DIPLOID_ALLELE) {
continue;
}
byte geno = genos.genotype(taxon, site);
//Check desired output and append the corresponding value
if (outputFormat.value() == OUTPUT_CHECK.c || outputFormat == null) {
if (geno == parentAGenos[site]) {
strB.append(",A");
} else if (geno == parentBGenos[site]) {
strB.append(",B");
} else if (geno == hets[0][site] || geno == hets[1][site]) {
strB.append(",H");
} else {
strB.append(",NA");
}
} else if (outputFormat.value() == OUTPUT_CHECK.i) {
if (geno == parentAGenos[site]) {
strB.append(",0");
} else if (geno == parentBGenos[site]) {
strB.append(",2");
} else if (geno == hets[0][site] || geno == hets[1][site]) {
strB.append(",1");
} else {
strB.append(",NA");
}
} else if (outputFormat.value() == OUTPUT_CHECK.r) {
if (geno == parentAGenos[site]) {
strB.append(",0");
} else if (geno == parentBGenos[site]) {
strB.append(",1");
} else if (geno == hets[0][site] || geno == hets[1][site]) {
strB.append(",0.5");
} else {
strB.append(",NA");
}
}
}
writeLine(strB, bw);
}
} catch (IOException e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("GenosToABHPlugin: writeConvertedGenos: Problem writing file: " + outfile() + ": " + e.getMessage());
}
}
private void writeLine(StringBuilder strB, BufferedWriter writer) {
try {
writer.write(strB.toString() + "\n");
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
@Override
public String getToolTipText() {
return "Convert Genotypes to A/B/H";
}
@Override
public ImageIcon getIcon() {
URL imageURL = GenosToABHPlugin.class.getResource("/net/maizegenetics/analysis/images/homozygous.gif");
if (imageURL == null) {
return null;
} else {
return new ImageIcon(imageURL);
}
}
@Override
public String getButtonName() {
return "ABH Genotype";
}
// public static void main(String[] args) {
// GeneratePluginCode.generate(GenosToABHPlugin.class);
// }
// The following getters and setters were auto-generated.
// Please use this method to re-generate.
//
// public static void main(String[] args) {
// GeneratePluginCode.generate(GenosToABHPlugin.class);
// }
/**
* Convenience method to run plugin with one return object.
*/
public GenotypeTable runPlugin(DataSet input) {
return (GenotypeTable) performFunction(input).getData(0).getData();
}
/**
* Output genotype file with ABH encoding
*
* @return Output file
*/
public String outfile() {
return outfile.value();
}
/**
* Set Output file. Output genotype file with ABH encoding
*
* @param value Output file
*
* @return this plugin
*/
public GenosToABHPlugin outfile(String value) {
outfile = new PluginParameter<>(outfile, value);
return this;
}
/**
* The full name of parent to be encoded as A
*
* @return Parent A
*/
public String parentA() {
return parentA.value();
}
/**
* Set Parent A. The full name of parent to be encoded as A
*
* @param value Parent A
*
* @return this plugin
*/
public GenosToABHPlugin parentA(String value) {
parentA = new PluginParameter<>(parentA, value);
return this;
}
/**
* The full name of parent to be encoded as B
*
* @return Parent B
*/
public String parentB() {
return parentB.value();
}
/**
* Set Parent B. The full name of parent to be encoded as B
*
* @param value Parent B
*
* @return this plugin
*/
public GenosToABHPlugin parentB(String value) {
parentB = new PluginParameter<>(parentB, value);
return this;
}
/**
* The output format enum
*
* @return Output Format
*/
public OUTPUT_CHECK outputFormat() {
return outputFormat.value();
}
/**
* Set Output Format. The output format enum
*
* @param value Output Format
*
* @return this plugin
*/
public GenosToABHPlugin outputFormat(OUTPUT_CHECK value) {
outputFormat = new PluginParameter<>(outputFormat, value);
return this;
}
@Override
public String getCitation() {
return "Stefan Reuscher, Jeff Glaubitz, Lynn Johnson (2015) First Annual TASSEL Hackathon";
}
@Override
public String pluginUserManualURL() {
return "https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/GenosToABH/GenosToABHPlugin";
}
}
