https://github.com/teerjk/VarSifter
Tip revision: 7e57e5857b08f5253f28e96477fc211f67a0ffea authored by Jamie K. Teer on 27 April 2020, 14:42:41 UTC
-Documentation updates to point to github.
-Documentation updates to point to github.
Tip revision: 7e57e58
SampleExporter.java
import java.awt.*;
import javax.swing.*;
import java.util.Map;
/**
* The SampleExporter class opens a dialog to determine what types of variants should be exported, and allows
* retrieval of results one line at a time (one per variant location) with those samples using the getNext() method.
*/
public class SampleExporter {
final String title = "<html>Select variant type(s).<p>Samples with variants of these types will be exported.</html>";
final String outTitle = "Select information to output.";
private JCheckBox homRefCB = new JCheckBox("Homozygous Reference");
private JCheckBox homVarCB = new JCheckBox("Homozygous Variant");
private JCheckBox hetVarCB = new JCheckBox("Heterozygous Variant");
private JCheckBox otherCB = new JCheckBox("Other");
private JCheckBox annotCB = new JCheckBox("Annotations");
private JCheckBox nameCB = new JCheckBox("Sample Name", true);
private JCheckBox[] genOptions = {homRefCB, homVarCB, hetVarCB, otherCB};
private JCheckBox[] outOptions;
private JTextField genScoreField = new JTextField(10);
private JTextField genScoreCovRatioField = new JTextField(10);
private boolean toFilter = false; //Only filter if this is true (ie, OK was clicked)
private VarData vdat;
private String[] annotNames;
private String[] names;
private String[] sampleValueName;
private AbstractMapper[] annotMapper;
private AbstractMapper[] sampleMapper;
private int[][] outData;
private int chrIndex;
private int lfIndex;
private int rfIndex;
private int refIndex;
private int varIndex;
private int mutTypeIndex;
private int indelIndex;
private int NA_Allele;
private int lastLine = 0;
/**
* Constructor assigns local fields needed from VarData object; will use currently filtered variant list!
* Then, opens dialog to determine which variant types are desired.
* @param inVDat VarData object
*/
public SampleExporter(VarData inVDat) {
this.vdat = inVDat;
annotNames = vdat.returnDataNames();
names = vdat.returnSampleNames();
Map<String, Integer> dataTypeAt = vdat.returnDataTypeAt();
annotMapper = vdat.returnAnnotMap();
sampleMapper = vdat.returnSampleMap();
outData = vdat.returnOutData();
chrIndex = dataTypeAt.get("Chr");
lfIndex = dataTypeAt.get("LeftFlank");
rfIndex = dataTypeAt.get("RightFlank");
refIndex = dataTypeAt.get("ref_allele");
varIndex = dataTypeAt.get("var_allele");
mutTypeIndex = dataTypeAt.get("muttype");
indelIndex = annotMapper[mutTypeIndex].getIndexOf("INDEL");
NA_Allele = sampleMapper[0].getIndexOf("NA");
VarSifter.setJComponentSize(genScoreField);
genScoreField.setText(Integer.toString(VarSifter.SCORE_THRESH));
VarSifter.setJComponentSize(genScoreCovRatioField);
genScoreCovRatioField.setText(Float.toString(VarSifter.SCORE_COV_THRESH));
JPanel scorePane = new JPanel();
scorePane.setLayout(new BoxLayout(scorePane, BoxLayout.X_AXIS));
scorePane.setAlignmentX(Component.LEFT_ALIGNMENT);
scorePane.add( new JLabel("Genotype Score Threshold: "));
scorePane.add(genScoreField);
JPanel scoreCovPane = new JPanel();
scoreCovPane.setLayout(new BoxLayout(scoreCovPane, BoxLayout.X_AXIS));
scoreCovPane.setAlignmentX(Component.LEFT_ALIGNMENT);
scoreCovPane.add( new JLabel("Genotype Score / Coverage Ratio Threshold: "));
scoreCovPane.add(genScoreCovRatioField);
JPanel filtPane = new JPanel();
filtPane.setLayout(new BoxLayout(filtPane, BoxLayout.Y_AXIS));
filtPane.add(scorePane);
filtPane.add(scoreCovPane);
//Set outOptions using available sample fields
this.sampleValueName = vdat.returnSampleValueNames();
outOptions = new JCheckBox[sampleValueName.length + 2];
outOptions[0] = annotCB;
outOptions[1] = nameCB;
for (int i=0; i<sampleValueName.length; i++) {
outOptions[i+2] = new JCheckBox(sampleValueName[i]);
}
Object[] params = {title, genOptions, new JSeparator(SwingConstants.HORIZONTAL), filtPane,
new JSeparator(SwingConstants.HORIZONTAL), outTitle, outOptions};
int opt = JOptionPane.showConfirmDialog(null, params, "Sample Export", JOptionPane.OK_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE);
if (opt == JOptionPane.OK_OPTION) {
toFilter = true;
}
}
/**
* Returns a header indicating which types of variants were desired (which checkboxes were checked)
* @return A String comment with the checked boxes
*/
public String getHeader() {
StringBuilder out = new StringBuilder("#Samples with the following variant types:\t");
for (JCheckBox cb : genOptions) {
if (cb.isSelected()) {
out.append(cb.getText() + "\t");
}
}
out.deleteCharAt(out.length() - 1);
out.append(VarSifter.newLine);
out.append("#Score_threshold: " + genScoreField.getText() + " score_coverage: " +
genScoreCovRatioField.getText());
if (annotCB.isSelected()) {
out.append(VarSifter.newLine);
for (String s : annotNames) {
out.append(s + "\t");
}
out.deleteCharAt(out.length() - 1);
}
return out.toString();
}
/**
* Returns the samples with previously selected genotype type(s) for the next variant line from the FILTERED vars.
* Returns null when nothing left to do (or nothing to do in first place.)
* Therefore, its best to call this function as if reading a file:
* SampleExporter se = new SampleExporter(Vardata v);
* String outLine;
* while ((outLine = se.getNextVariant()) != null) {
* //do stuff
* }
* @return A tab-delim String with location, semi-colon delimited info for each sample.
*/
public String getNextVariant() {
if (! toFilter || lastLine >= outData.length) {
return null;
}
int scoreT;
float scoreCovT;
try {
scoreT = Integer.parseInt(genScoreField.getText());
scoreCovT = Float.parseFloat(genScoreCovRatioField.getText());
}
catch (NumberFormatException nfe) {
VarSifter.showError("<html>You have entered an inappropriate number in Sample Export window!<p>" +
"Please use an integer for Genotype Score, and a floating point number for " +
"Score/Cov Ratio.</html");
System.out.println(nfe);
return null;
}
String refAllele = annotMapper[refIndex].getString(outData[lastLine][refIndex]);
String varAllele = annotMapper[varIndex].getString(outData[lastLine][varIndex]);
int homRefGen;
int homVarGen;
int muttype = outData[lastLine][mutTypeIndex];
if (muttype == indelIndex || refAllele.length() > 1) {
homRefGen = sampleMapper[0].getIndexOf(refAllele + ":" + refAllele);
homVarGen = sampleMapper[0].getIndexOf(varAllele + ":" + varAllele);
}
else {
homRefGen = sampleMapper[0].getIndexOf(refAllele + refAllele);
homVarGen = sampleMapper[0].getIndexOf(varAllele + varAllele);
}
StringBuilder outTemp = new StringBuilder();
int[][] sampDataLine = vdat.returnSample(lastLine);
if (annotCB.isSelected()) {
for (int ind=0; ind < annotNames.length; ind++) {
outTemp.append(annotMapper[ind].getString(outData[lastLine][ind]) + "\t");
}
}
else {
for (int ind : new int[]{chrIndex, lfIndex, rfIndex, refIndex, varIndex, mutTypeIndex}) {
outTemp.append(annotMapper[ind].getString(outData[lastLine][ind]) + "\t");
}
}
for (int j=0; j<names.length; j++) {
int sampGen = sampDataLine[j][1];
//qual filters - procede on success ("continue" otherwise)
if ((sampleMapper[1].getDataType() == VarData.INTEGER &&
sampDataLine[j][2] >= scoreT &&
((float)sampDataLine[j][2] / sampDataLine[j][3]) >= scoreCovT) ||
(sampleMapper[1].getDataType() == VarData.FLOAT &&
sampleMapper[1].getFloat(sampDataLine[j][2]) >= scoreT &&
(sampleMapper[1].getFloat(sampDataLine[j][2]) / sampDataLine[j][3]) >= scoreCovT)
) {
//Proceed
}
else {
continue;
}
//homnonref
if (homRefCB.isSelected() && sampGen == homRefGen) {
outTemp.append( fetchSampleInfo(j, sampDataLine) + "\t");
continue;
}
//homvar
if (homVarCB.isSelected() && sampGen == homVarGen) {
outTemp.append( fetchSampleInfo(j, sampDataLine) + "\t");
continue;
}
//hetvar and other
if ((hetVarCB.isSelected()
|| otherCB.isSelected()) && sampGen != homRefGen && sampGen != homVarGen
&& sampGen != NA_Allele) {
boolean hasVar = false;
String[] alleles;
if (muttype == indelIndex || refAllele.length() > 1) {
alleles = sampleMapper[0].getString(sampGen).split(":");
}
else {
alleles = sampleMapper[0].getString(sampGen).split("");
}
for (String s : alleles) {
if (s.equals(varAllele)) {
hasVar = true;
}
}
if (hetVarCB.isSelected() && hasVar) {
outTemp.append( fetchSampleInfo(j, sampDataLine) + "\t");
continue;
}
else if (otherCB.isSelected() && !hasVar) {
outTemp.append( fetchSampleInfo(j, sampDataLine) + "\t");
continue;
}
}
}
lastLine++;
outTemp.deleteCharAt(outTemp.length() - 1);
return outTemp.toString();
}
/**
* Get sample info, return as semicolon delimited string
* @param sampIndex The sample index (0-based)
* @param sampLine The 2d array of sample output [sampIndex][info_type(sample_name, genotype, score, coverage)]
*/
private String fetchSampleInfo(int sampIndex, int[][] sampLine) {
StringBuilder outString = new StringBuilder();
if (nameCB.isSelected()) {
outString.append(names[sampIndex] + ";"); //Sample name!
}
for (int i=0; i<sampleValueName.length; i++) {
// Check whether to output; Add 2 to outOptions index (as annotation and name have been added to beginning)
if (outOptions[i+2].isSelected()) {
// Add 1 to sampLine second dimension (sampIndex[][THIS]), as the name has been added to beginning.
outString.append(sampleMapper[i].getString(sampLine[sampIndex][i+1]) + ";");
}
}
if (outString.length() > 0) {
outString.deleteCharAt(outString.length() - 1);
}
return outString.toString();
}
}
