eqtlmappingpipeline.binarymeta.meta.MetaAnalysisResultThread Maven / Gradle / Ivy
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package eqtlmappingpipeline.binarymeta.meta;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.EQTL;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.concurrent.LinkedBlockingQueue;
/**
* @author harmjan
*/
public class MetaAnalysisResultThread extends Thread {
private final LinkedBlockingQueue m_queue_input;
// private double pvaluethreshold = 1;
private static String header = "PValue\t"
+ "SNPName\t"
+ "SNPChr\t"
+ "SNPChrPos\t"
+ "ProbeName\t"
+ "ProbeChr\t"
+ "ProbeCenterChrPos\t"
+ "CisTrans\t"
+ "SNPType\t"
+ "AlleleAssessed\t"
+ "OverallZScore\t"
+ "DatasetsWhereSNPProbePairIsAvailableAndPassesQC\t"
+ "DatasetsZScores\t"
+ "DatasetsNrSamples\t"
+ "IncludedDatasetsMeanProbeExpression\t"
+ "IncludedDatasetsProbeExpressionVariance\t"
+ "HGNCName\t"
+ "IncludedDatasetsCorrelationCoefficient";
private int ctr = 0;
private EQTL[] eQTLBuffer = new EQTL[100000];
private EQTL[] finalEQTLBuffer = new EQTL[0];
private int nrInFinalBuffer = 0;
private static MetaSettings m_settings;
private int perm;
private String[] datasets;
private final TextFile zscoretable;
private final PValueThreshold pvaluethreshold;
private final ArrayList snps;
private final HashMap> snpProbeSelection;
private final ArrayList probes;
public MetaAnalysisResultThread(LinkedBlockingQueue input,
MetaSettings m_settings,
String[] datasets,
int perm,
TextFile zscoretable, PValueThreshold p, ArrayList snps, HashMap> snpProbeSelection, ArrayList probes) {
this.m_settings = m_settings;
this.datasets = datasets;
this.perm = perm;
this.zscoretable = zscoretable;
this.pvaluethreshold = p;
m_queue_input = input;
this.snps = snps;
this.snpProbeSelection = snpProbeSelection;
this.probes = probes;
}
TextFile snpout = null;
@Override
public void run() {
boolean poison = false;
try {
snpout = new TextFile(m_settings.getOutput() + "snpsandnreqtls.txt", TextFile.W);
while (!poison) {
try {
MetaAnalysisWorkPackage pack = m_queue_input.take();
if (!pack.getPoison()) {
Integer snpnum = pack.getSNPNum();
String snp = snps.get(snpnum);
if (snpProbeSelection == null || snpProbeSelection.containsKey(snp)) {
analyze(pack);
}
// if(taken % printperiterations == 0){
// System.out.println("Thread "+this.getName()+" calculated "+taken+" workpackages.");
// }
} else {
poison = pack.getPoison();
// System.out.println("Thread " + m_name + " got killed by a poisonous workpackage, but was bravely able to perform\t" + testsPerformed + "\ttests");
}
} catch (InterruptedException ex) {
ex.printStackTrace();
}
}
if (ctr > 0) {
mergebuffers(ctr);
}
snpout.close();
java.util.Arrays.sort(finalEQTLBuffer);
// write eQTL results..
writeresults();
TextFile out = new TextFile(m_settings.getOutput() + "/NumberOfEQTLSTotal.txt", TextFile.W);
out.writeln("Number of eQTLs in total: " + totalNumberOfEQTLs);
System.out.println("Number of eQTLs in total: " + totalNumberOfEQTLs);
out.writeln("Number of snps in total: " + uniqueSNPs.size());
out.writeln("Number of snps in total not passing QC: " + uniqueSNPsNotPassingQC.size());
System.out.println("Number of snps in total: " + uniqueSNPs.size());
TextFile out2 = new TextFile(m_settings.getOutput() + "/TestedSNPs.txt", TextFile.W);
List list = new ArrayList(uniqueSNPs);
out2.writeList(list);
out2.close();
out2 = new TextFile(m_settings.getOutput() + "/TestedSNPsNPQC.txt", TextFile.W);
list = new ArrayList(uniqueSNPsNotPassingQC);
out2.writeList(list);
out.writeln("Number of probes in total: " + uniqueProbes.size());
System.out.println("Number of probes in total: " + uniqueProbes.size());
out2 = new TextFile(m_settings.getOutput() + "/TestedProbes.txt", TextFile.W);
List list2 = new ArrayList(uniqueProbes);
ArrayList list2str = new ArrayList();
for (Integer i : list2) {
list2str.add("" + i);
}
out2.writeList(list2str);
out.close();
} catch (IOException e) {
e.printStackTrace();
}
}
private HashSet uniqueSNPs = new HashSet();
private HashSet uniqueSNPsNotPassingQC = new HashSet();
private HashSet uniqueProbes = new HashSet();
private int totalNumberOfEQTLs = 0;
private void analyze(MetaAnalysisWorkPackage pack) {
Integer snpnum = pack.getSNPNum();
String snp = snps.get(snpnum).intern();
HashSet allowedProbes = null;
if (snpProbeSelection != null) {
allowedProbes = snpProbeSelection.get(snp);
}
Integer[] probeList = pack.getListOfTestedProbes();
for (int i = 0; i < probeList.length; i++) {
String probe = probes.get(probeList[i]);
if (probe != null && (allowedProbes == null || allowedProbes.contains(probe))) {
totalNumberOfEQTLs++;
uniqueProbes.add(probeList[i]);
}
}
if (pack.getPassedQC()) {
uniqueSNPs.add(snps.get(snpnum).intern());
} else {
uniqueSNPsNotPassingQC.add(snps.get(snpnum).intern());
}
if (m_settings.isMakezscoretable() && zscoretable != null) {
try {
String zscoreout = pack.getZScoreOut();
if (zscoreout != null) {
zscoretable.writeln(zscoreout);
pack.setZScoreOut(null);
}
} catch (IOException e) {
e.printStackTrace();
}
}
EQTL[] finalEQTLs = pack.getResult();
int nreQTLsForSNP = 0;
for (int p = 0; p < finalEQTLs.length; p++) {
// if (finalEQTLs[p] != null) {
//// uniqueProbes.add(finalEQTLs[p].getProbe());
// }
if (finalEQTLs[p] != null && finalEQTLs[p].getPvalue() <= pvaluethreshold.getPvalue() && (allowedProbes == null || allowedProbes.contains(finalEQTLs[p].getProbe()))) {
nreQTLsForSNP++;
// check cis / trans constraints ...
// if(finalEQTLs[p].getProbeChr())
// boolean includeEQTL = true;
// if(transAnalysis && !cisAnalysis){
// if(finalEQTLs[p].getProbeChr().byteValue() == -1 || finalEQTLs[p].getRsChr().byteValue() == -1){
// includeEQTL = false;
// }
// if(finalEQTLs[p].getProbeChrPos().intValue() == -1 || finalEQTLs[p].getRsChr().byteValue() == -1){
// includeEQTL = false;
// }
// if(finalEQTLs[p].getProbeChr().byteValue() == finalEQTLs[p].getRsChr().byteValue()){
// if( Math.abs(finalEQTLs[p].getProbeChr().byteValue() - finalEQTLs[p].getRsChr().byteValue()) < cisProbeDistance){
// includeEQTL = false;
// }
// }
// }
// if (includeEQTL) {
eQTLBuffer[ctr] = finalEQTLs[p];
ctr++;
if (ctr == eQTLBuffer.length) {
mergebuffers(ctr);
ctr = 0;
// System.out.println("SNPs tested: "+s+"/"+snps.size()+", threshold: "+pvaluethreshold);
}
// }
} else {
if (finalEQTLs[p] != null) {
finalEQTLs[p].clearData();
finalEQTLs[p] = null;
}
}
}
finalEQTLs = null;
try {
snpout.writeln(snps.get(pack.getSNPNum()) + "\t" + nreQTLsForSNP);
} catch (Exception e) {
e.printStackTrace();
}
pack.clearData();
pack = null;
}
protected void mergebuffers(int ctr) {
EQTL[] toMerge = null;
if (ctr < eQTLBuffer.length) {
toMerge = new EQTL[ctr];
System.arraycopy(eQTLBuffer, 0, toMerge, 0, ctr);
} else {
toMerge = eQTLBuffer;
}
EQTL[] tmp = new EQTL[finalEQTLBuffer.length + toMerge.length];
System.arraycopy(toMerge, 0, tmp, 0, toMerge.length);
System.arraycopy(finalEQTLBuffer, 0, tmp, toMerge.length, finalEQTLBuffer.length);
nrInFinalBuffer += toMerge.length;
if (nrInFinalBuffer < m_settings.getFinalEQTLBufferMaxLength()) {
finalEQTLBuffer = tmp;
} else {
java.util.Arrays.sort(tmp);
finalEQTLBuffer = new EQTL[m_settings.getFinalEQTLBufferMaxLength()];
// System.out.println(finalEQTLBuffer.length+"\t"+tmp.length);
System.arraycopy(tmp, 0, finalEQTLBuffer, 0, m_settings.getFinalEQTLBufferMaxLength());
nrInFinalBuffer = m_settings.getFinalEQTLBufferMaxLength();
pvaluethreshold.setPvalue(finalEQTLBuffer[nrInFinalBuffer - 1].getPvalue());
}
}
private void writeresults() throws IOException {
TextFile out = null;
if (perm > 0) {
out = new TextFile(m_settings.getOutput() + "PermutedEQTLsPermutationRound" + perm + ".txt.gz", TextFile.W);
} else {
out = new TextFile(m_settings.getOutput() + "eQTLs.txt.gz", TextFile.W);
}
out.write(header + "\n");
for (int i = 0; i < finalEQTLBuffer.length; i++) {
finalEQTLBuffer[i].setDatasets(datasets);
out.writeln(finalEQTLBuffer[i].toString());
}
out.close();
TextFile oppositeEffects = null;
if (perm > 0) {
oppositeEffects = new TextFile(m_settings.getOutput() + "OppositeEffects-PermutedEQTLsPermutationRound" + perm + ".txt.gz", TextFile.W);
} else {
oppositeEffects = new TextFile(m_settings.getOutput() + "OppositeEffects-eQTLs.txt", TextFile.W);
}
for (int i = 0; i < finalEQTLBuffer.length; i++) {
String oppositeEffectIndicator = "";
double pValueOverall = finalEQTLBuffer[i].getPvalue();
double pValueAbs = finalEQTLBuffer[i].getPvalueAbs();
if (pValueAbs < pValueOverall) {
oppositeEffectIndicator = "OppositeEffect";
if (pValueAbs <= pValueOverall / 100000) {
oppositeEffectIndicator = "StrongOppositeEffect";
}
oppositeEffects.writeln(oppositeEffectIndicator + "\t" + pValueAbs + "\t" + finalEQTLBuffer[i].getZscoreAbs() + "\t" + finalEQTLBuffer[i].toString());
}
}
oppositeEffects.close();
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy