nl.umcg.westrah.binarymetaanalyzer.BinaryMetaAnalysisDataset Maven / Gradle / Ivy
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package nl.umcg.westrah.binarymetaanalyzer;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.nio.ByteBuffer;
import java.util.ArrayList;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.bin.BinaryFile;
import umcg.genetica.io.text.TextFile;
/**
*
* @author Harm-Jan
*/
public class BinaryMetaAnalysisDataset {
private boolean isCisDataset = false;
private final String datasetLoc;
private MetaQTL4MetaTrait[][] snpCisProbeMap;
private long[] snpBytes;
private String[] alleles;
private String[] allelesAssessed;
private String[] minorAlleles;
private int[] n;
private double[] callrates;
private double[] hwes;
private double[] mafs;
private String[] probeList;
private String[] snps;
private final MetaQTL4TraitAnnotation probeAnnotation;
private final int platformId;
private RandomAccessFile raf;
private String name = null;
private String platform = null;
public BinaryMetaAnalysisDataset(String dir, String name, String prefix, int permutation, String platform, MetaQTL4TraitAnnotation probeAnnotation) throws IOException {
dir = Gpio.formatAsDirectory(dir);
String matrix = dir;
String probeFile = dir;
String snpFile = dir;
this.platform = platform;
this.name = name;
this.probeAnnotation = probeAnnotation;
this.platformId = probeAnnotation.getPlatformId(platform);
String pref = "Dataset";
if (prefix != null) {
pref = prefix;
}
if (permutation > 0) {
matrix += pref + "-PermutationRound-" + permutation + ".dat";
probeFile += pref + "-PermutationRound-" + permutation + "-ColNames.txt.gz";
snpFile += pref + "-PermutationRound-" + permutation + "-RowNames.txt.gz";
} else {
matrix += pref + ".dat";
probeFile += pref + "-ColNames.txt.gz";
snpFile += pref + "-RowNames.txt.gz";
}
this.datasetLoc = dir;
// check presence of files
if (!Gpio.exists(matrix)) {
throw new IOException("Could not find file: " + matrix);
}
if (!Gpio.exists(probeFile)) {
throw new IOException("Could not find file: " + probeFile);
}
if (!Gpio.exists(snpFile)) {
throw new IOException("Could not find file: " + snpFile);
}
BinaryFile f = new BinaryFile(matrix, BinaryFile.R);
int firstInt = f.readInt();
f.close();
isCisDataset = (firstInt == 1);
System.out.println("Matrix: " + matrix);
System.out.println("SNPFile: " + snpFile);
System.out.println("ProbeFile: " + probeFile);
if (isCisDataset) {
System.out.println("This dataset is a cis- dataset.");
} else {
System.out.println("This dataset is a full size dataset.");
}
loadSNPs(snpFile);
System.out.println(snps.length + " SNPs loaded");
loadProbes(probeFile);
System.out.println(probeList.length + " probes loaded");
raf = new RandomAccessFile(matrix, "r");
}
private void loadSNPs(String snpFile) throws IOException {
// get nr of lines
TextFile tf = new TextFile(snpFile, TextFile.R);
tf.readLine(); // skip header
int nrSNPs = tf.countLines();
tf.close();
System.out.println(snpFile + "\t has " + nrSNPs + " SNPs");
snpBytes = new long[nrSNPs];
alleles = new String[nrSNPs];
allelesAssessed = new String[nrSNPs];
minorAlleles = new String[nrSNPs];
n = new int[nrSNPs];
callrates = new double[nrSNPs];
hwes = new double[nrSNPs];
mafs = new double[nrSNPs];
if (isCisDataset) {
// jagged array, hurrah
snpCisProbeMap = new MetaQTL4MetaTrait[nrSNPs][0];
}
tf.open();
tf.readLine(); // skip header
String[] elems = tf.readLineElems(TextFile.tab);
int ln = 0;
snps = new String[nrSNPs];
snpBytes[0] = 4; // account for magic number.
while (elems != null) {
String snp = new String(elems[0].getBytes("UTF-8")).intern();
String allelesStr = new String(elems[1].getBytes("UTF-8")).intern();
String minorAlleleStr = new String(elems[2].getBytes("UTF-8")).intern();
String alleleAssessedStr = new String(elems[3].getBytes("UTF-8")).intern();
snps[ln] = snp;
alleles[ln] = allelesStr;
allelesAssessed[ln] = alleleAssessedStr;
minorAlleles[ln] = minorAlleleStr;
int nrCalled = 0;
double maf = 0;
double cr = 0;
double hwe = 0;
int nrZScores = 0;
try {
nrCalled = Integer.parseInt(elems[4]);
} catch (NumberFormatException e) {
System.err.println("ERROR: nrCalled is not an int (input: " + elems[4] + ") for dataset: " + datasetLoc + " on line: " + ln);
}
try {
maf = Double.parseDouble(elems[5]);
} catch (NumberFormatException e) {
System.err.println("ERROR: maf is not a double (" + elems[5] + ") for dataset: " + datasetLoc + " on line: " + ln);
}
try {
cr = Double.parseDouble(elems[6]);
} catch (NumberFormatException e) {
System.err.println("ERROR: cr is not a double (" + elems[6] + ") for dataset: " + datasetLoc + " on line: " + ln);
}
try {
hwe = Double.parseDouble(elems[7]);
} catch (NumberFormatException e) {
System.err.println("ERROR: hwe is not a double (" + elems[7] + ") for dataset: " + datasetLoc + " on line: " + ln);
}
try {
nrZScores = Integer.parseInt(elems[8]);
} catch (NumberFormatException e) {
System.err.println("ERROR: nrZScores is not an int (input: " + elems[8] + ") for dataset: " + datasetLoc + " on line: " + ln);
}
n[ln] = nrCalled;
callrates[ln] = cr;
hwes[ln] = hwe;
mafs[ln] = maf;
if (ln + 1 < nrSNPs) {
snpBytes[ln + 1] = snpBytes[ln] + (nrZScores * 4);
}
if (isCisDataset) {
MetaQTL4MetaTrait[] snpProbeList = new MetaQTL4MetaTrait[(elems.length - 9)];
for (int e = 9; e < elems.length; e++) {
// get the list of probes for this particular SNP.
String probe = elems[e];
MetaQTL4MetaTrait t = probeAnnotation.getTraitForPlatformId(platformId, probe);
// System.out.println(snp+"\t"+elems[e]);
snpProbeList[e - 9] = t;
}
snpCisProbeMap[ln] = snpProbeList;
}
elems = tf.readLineElems(TextFile.tab);
ln++;
}
tf.close();
}
private void loadProbes(String columns) throws IOException {
TextFile tf = new TextFile(columns, TextFile.R);
// nrProbes = tf.countLines();
// tf.close();
//
// tf.open();
ArrayList allProbes = tf.readAsArrayList();
tf.close();
probeList = allProbes.toArray(new String[0]);
}
public MetaQTL4MetaTrait[] getCisProbes(int snp) {
return snpCisProbeMap[snp];
}
public float[] getZScores(int snp) throws IOException {
long snpBytePos = snpBytes[snp];
long snpByteNextPos = 0;
if (snp == snpBytes.length - 1) {
snpByteNextPos = raf.length();
} else {
snpByteNextPos = snpBytes[snp + 1];
}
//
// if (snpCisProbeMap != null) {
// nrZ = snpCisProbeMap[snp].length;
// }
// System.out.println(snp + "\t" + snpBytePos + "\t" + snpByteNextPos);
raf.seek(snpBytePos);
int readlen = (int) (snpByteNextPos - snpBytePos);
byte[] bytesToRead = new byte[readlen];
raf.read(bytesToRead);
ByteBuffer bytebuffer = ByteBuffer.wrap(bytesToRead);
float[] output = new float[readlen / 4];
for (int i = 0; i < output.length; i++) {
output[i] = bytebuffer.getFloat();
}
return output;
}
public String[] getSNPs() {
return snps;
}
public String[] getProbeList() {
return probeList;
}
public int getSampleSize(int datasetSNPId) {
return n[datasetSNPId];
}
public String getAlleles(int datasetSNPId) {
return alleles[datasetSNPId];
}
public String getAlleleAssessed(int datasetSNPId) {
return allelesAssessed[datasetSNPId];
}
public boolean getIsCisDataset() {
return isCisDataset;
}
public void close() throws IOException {
raf.close();
}
public String getName() {
return name;
}
public String getPlatform() {
return platform;
}
}
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