eqtlmappingpipeline.util.GenotypeDataQuery Maven / Gradle / Ivy
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package eqtlmappingpipeline.util;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.SNP;
import umcg.genetica.io.trityper.SNPLoader;
import umcg.genetica.io.trityper.TriTyperGenotypeData;
import umcg.genetica.io.trityper.util.BaseAnnot;
/**
*
* @author harmjan
*/
public class GenotypeDataQuery {
public void getSNPsInRegion(String dataset, int chr, int positionA, int positionB) {
if (positionB < positionA) {
int tmp = positionA;
positionA = positionB;
positionB = tmp;
}
try {
TriTyperGenotypeData tgd = new TriTyperGenotypeData();
tgd.load(dataset);
String[] snps = tgd.getSNPs();
int pos = 0;
for (String s : snps) {
int snpchr = tgd.getChr(pos);
int snppos = tgd.getChrPos(pos);
if (snpchr == chr && snppos >= positionA && snppos <= positionB) {
System.out.println(s + "\t" + chr + "\t" + snppos);
}
pos++;
}
} catch (Exception e) {
e.printStackTrace();
}
}
public void getSNPMAF(String dataset, String snpfile) {
try {
TriTyperGenotypeData tgd = new TriTyperGenotypeData();
tgd.load(dataset);
TextFile tf = new TextFile(snpfile, TextFile.R);
String[] snpstoquery = tf.readAsArray();
tf.close();
SNPLoader loader = tgd.createSNPLoader();
for (String snp : snpstoquery) {
Integer snpid = tgd.getSnpToSNPId().get(snp);
if (snpid == -9) {
System.out.println("SNP " + snp + " does not exist in dataset");
} else {
SNP snpObj = tgd.getSNPObject(snpid);
loader.loadGenotypes(snpObj);
System.out.println(snp + "\t" + BaseAnnot.toString(snpObj.getAlleles()[0])
+ "/" + BaseAnnot.toString(snpObj.getAlleles()[1])
+ "\t" + BaseAnnot.toString(snpObj.getMinorAllele())
+ "\t" + snpObj.getMAF());
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
public void getSNPStatsForAllSNPs(String dataset) {
try {
TriTyperGenotypeData tgd = new TriTyperGenotypeData();
tgd.load(dataset);
SNPLoader loader = tgd.createSNPLoader();
String[] snpstoquery = tgd.getSNPs();
if (loader.hasDosageInformation()) {
System.out.println("SNP\tAlleles\tMinorAllele\tMAF\tDosageMAF\tCR\tHWEP\tNumAA\tNumAB\tNumBB\tTotalCalled\tNotCalled");
} else {
System.out.println("SNP\tAlleles\tMinorAllele\tMAF\tCR\tHWEP\tNumAA\tNumAB\tNumBB\tTotalCalled\tNotCalled");
}
for (String snp : snpstoquery) {
Integer snpid = tgd.getSnpToSNPId().get(snp);
if (snpid == -9) {
System.out.println("SNP " + snp + " does not exist in dataset");
} else {
SNP snpObj = tgd.getSNPObject(snpid);
loader.loadGenotypes(snpObj);
if (loader.hasDosageInformation()) {
loader.loadDosage(snpObj);
}
int nrGenotypes = 0;
int numNULL = 0;
int numAA = 0;
int numAB = 0;
int numBB = 0;
byte[] genotypes = snpObj.getGenotypes();
for (int g = 0; g < genotypes.length; g++) {
switch (genotypes[g]) {
case -1:
numNULL++;
break;
case 0:
numAA++;
nrGenotypes++;
break;
case 1:
numAB++;
nrGenotypes++;
break;
case 2:
numBB++;
nrGenotypes++;
break;
}
}
if (loader.hasDosageInformation()) {
System.out.println(snp + "\t" + BaseAnnot.toString(snpObj.getAlleles()[0])
+ "/" + BaseAnnot.toString(snpObj.getAlleles()[1])
+ "\t" + BaseAnnot.toString(snpObj.getMinorAllele())
+ "\t" + snpObj.getMAF()
+ "\t" + snpObj.getDosageMAF()
+ "\t" + snpObj.getCR()
+ "\t" + snpObj.getHWEP()
+ "\t" + numAA
+ "\t" + numAB
+ "\t" + numBB
+ "\t" + nrGenotypes
+ "\t" + numNULL);
} else {
System.out.println(snp + "\t" + BaseAnnot.toString(snpObj.getAlleles()[0])
+ "/" + BaseAnnot.toString(snpObj.getAlleles()[1])
+ "\t" + BaseAnnot.toString(snpObj.getMinorAllele())
+ "\t" + snpObj.getMAF()
+ "\t" + snpObj.getCR()
+ "\t" + snpObj.getHWEP()
+ "\t" + numAA
+ "\t" + numAB
+ "\t" + numBB
+ "\t" + nrGenotypes
+ "\t" + numNULL);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
void getSNPStatsForAllSNPs(String dataset, String in2) {
try {
TriTyperGenotypeData tgd = new TriTyperGenotypeData();
tgd.load(dataset);
SNPLoader loader = tgd.createSNPLoader();
String[] snpstoquery = new String[]{in2};
if (loader.hasDosageInformation()) {
System.out.println("SNP\tAlleles\tMinorAllele\tMAF\tDosageMAF\tCR\tHWEP\tNumAA\tNumAB\tNumBB\tTotalCalled\tNotCalled");
} else {
System.out.println("SNP\tAlleles\tMinorAllele\tMAF\tCR\tHWEP\tNumAA\tNumAB\tNumBB\tTotalCalled\tNotCalled");
}
for (String snp : snpstoquery) {
Integer snpid = tgd.getSnpToSNPId().get(snp);
if (snpid == -9) {
System.out.println("SNP " + snp + " does not exist in dataset");
} else {
SNP snpObj = tgd.getSNPObject(snpid);
loader.loadGenotypes(snpObj);
if (loader.hasDosageInformation()) {
loader.loadDosage(snpObj);
}
int nrGenotypes = 0;
int numNULL = 0;
int numAA = 0;
int numAB = 0;
int numBB = 0;
byte[] genotypes = snpObj.getGenotypes();
for (int g = 0; g < genotypes.length; g++) {
switch (genotypes[g]) {
case -1:
numNULL++;
break;
case 0:
numAA++;
nrGenotypes++;
break;
case 1:
numAB++;
nrGenotypes++;
break;
case 2:
numBB++;
nrGenotypes++;
break;
}
}
if (loader.hasDosageInformation()) {
System.out.println(snp + "\t" + BaseAnnot.toString(snpObj.getAlleles()[0])
+ "/" + BaseAnnot.toString(snpObj.getAlleles()[1])
+ "\t" + BaseAnnot.toString(snpObj.getMinorAllele())
+ "\t" + snpObj.getMAF()
+ "\t" + snpObj.getDosageMAF()
+ "\t" + snpObj.getCR()
+ "\t" + snpObj.getHWEP()
+ "\t" + numAA
+ "\t" + numAB
+ "\t" + numBB
+ "\t" + nrGenotypes
+ "\t" + numNULL);
} else {
System.out.println(snp + "\t" + BaseAnnot.toString(snpObj.getAlleles()[0])
+ "/" + BaseAnnot.toString(snpObj.getAlleles()[1])
+ "\t" + BaseAnnot.toString(snpObj.getMinorAllele())
+ "\t" + snpObj.getMAF()
+ "\t" + snpObj.getCR()
+ "\t" + snpObj.getHWEP()
+ "\t" + numAA
+ "\t" + numAB
+ "\t" + numBB
+ "\t" + nrGenotypes
+ "\t" + numNULL);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
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