net.maizegenetics.taxa.distance.ReadDistanceMatrix Maven / Gradle / Ivy
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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.
//
// ReadDistanceMatrix.java
//
package net.maizegenetics.taxa.distance;
import net.maizegenetics.taxa.TaxaList;
import net.maizegenetics.taxa.TaxaListBuilder;
import net.maizegenetics.taxa.Taxon;
import net.maizegenetics.util.GeneralAnnotationStorage;
import net.maizegenetics.util.Utils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.util.regex.Pattern;
/**
* @author Terry Casstevens
*/
public class ReadDistanceMatrix {
private static final Logger myLogger = LogManager.getLogger(ReadDistanceMatrix.class);
private static final Pattern WHITESPACE_PATTERN = Pattern.compile("\\s+");
private ReadDistanceMatrix() {
}
public static DistanceMatrix readDistanceMatrix(String filename) {
String[] grmFilenames = DistanceMatrixUtils.getGRMFilenames(filename);
String grmNBinFilename = grmFilenames[2];
try (BufferedReader reader = Utils.getBufferedReader(filename)) {
GeneralAnnotationStorage.Builder annotations = GeneralAnnotationStorage.getBuilder();
boolean notFinished = true;
String line = null;
while (notFinished) {
line = reader.readLine();
if (line == null) {
throw new IllegalArgumentException("ReadDistanceMatrix: There is no matrix data in this file: " + filename);
}
line = line.trim();
if (line.isEmpty()) {
// do nothing
} else if (line.startsWith("##")) {
String[] keyValue = line.substring(2).split("=", 2);
annotations.addAnnotation(keyValue[0].trim(), keyValue[1].trim());
} else {
notFinished = false;
}
}
int numTaxa = 0;
try {
numTaxa = Integer.parseInt(line);
} catch (NumberFormatException e) {
throw new IllegalArgumentException("ReadDistanceMatrix: The number of taxa is not a number: " + line);
}
DistanceMatrixBuilder builder = DistanceMatrixBuilder.getInstance(numTaxa);
builder.annotation(annotations.build());
String current = reader.readLine();
int index = 0;
while (current != null) {
if (index >= numTaxa) {
throw new IllegalArgumentException("ReadDistancMatrix: There are too many lines in this file. Expected: " + (numTaxa + 1) + " counting the first line (number of taxa)");
}
String[] tokens = WHITESPACE_PATTERN.split(current);
if (tokens.length != numTaxa + 1) {
throw new IllegalStateException("ReadDistanceMatrix: Incorrect number of values on line number: " + (index + 2) + " expected: " + (numTaxa + 1) + " counting taxon name. actual: " + tokens.length);
}
builder.addTaxon(new Taxon(tokens[0]));
for (int i = 0; i < numTaxa; i++) {
try {
builder.set(index, i, Double.parseDouble(tokens[i + 1]));
} catch (NumberFormatException nfex) {
myLogger.debug(nfex.getMessage(), nfex);
throw new IllegalArgumentException("ReadDistanceMatrix: Incorrectly formatted number: " + tokens[i + 1] + " on line number: " + (index + 2));
}
}
current = reader.readLine();
index++;
}
if (index != numTaxa) {
throw new IllegalArgumentException("ReadDistanceMatrix: There are too few lines in this file. Expected: " + (numTaxa + 1) + " counting the first line (number of taxa)");
}
if (new File(grmNBinFilename).exists()) {
readBinMultiBlupCounts(grmNBinFilename, builder);
}
return builder.build();
} catch (IOException ioex) {
myLogger.debug(ioex.getMessage(), ioex);
throw new IllegalStateException("ReadDistanceMatrix: Problem reading file: " + filename);
}
}
public static DistanceMatrix readBinMultiBlupMatrix(String filename) {
String[] grmFilenames = DistanceMatrixUtils.getGRMFilenames(filename);
String grmIdFilename = grmFilenames[0];
String grmBinFilename = grmFilenames[1];
String grmNBinFilename = grmFilenames[2];
TaxaList taxa = readBinMultiBlupID(grmIdFilename);
int numTaxa = taxa.numberOfTaxa();
DistanceMatrixBuilder builder = DistanceMatrixBuilder.getInstance(taxa);
int taxaOne = 0;
int taxaTwo = 0;
try (InputStream input = Utils.getInputStream(grmBinFilename)) {
byte[] current = new byte[4];
int numRead = input.read(current);
while (numRead == 4) {
float f = ByteBuffer.wrap(current).order(ByteOrder.LITTLE_ENDIAN).getFloat();
builder.set(taxaTwo, taxaOne++, f);
if (taxaOne > taxaTwo) {
taxaOne = 0;
taxaTwo++;
}
numRead = input.read(current);
}
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("ReadDistanceMatrix: readBinMultiBlupMatrix: Problem reading: " + grmBinFilename);
}
readBinMultiBlupCounts(grmNBinFilename, builder);
return builder.build();
}
public static TaxaList readBinMultiBlupID(String filename) {
TaxaListBuilder builder = new TaxaListBuilder();
try (BufferedReader reader = Utils.getBufferedReader(filename)) {
String current = reader.readLine();
while (current != null) {
String[] tokens = current.split("\t");
if (tokens.length != 2) {
throw new IllegalStateException("ReadDistanceMatrix: readBinMultiBlupID: Rows must have two columns: " + filename);
}
builder.add(new Taxon(tokens[1]));
current = reader.readLine();
}
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("ReadDistanceMatrix: readBinMultiBlupID: Problem reading: " + filename);
}
return builder.build();
}
public static void readBinMultiBlupCounts(String filename, DistanceMatrixBuilder builder) {
try (InputStream input = Utils.getInputStream(filename)) {
int taxaOne = 0;
int taxaTwo = 0;
byte[] current = new byte[4];
int numRead = input.read(current);
while (numRead == 4) {
float f = ByteBuffer.wrap(current).order(ByteOrder.LITTLE_ENDIAN).getFloat();
builder.setCount(taxaTwo, taxaOne++, Math.round(f));
if (taxaOne > taxaTwo) {
taxaOne = 0;
taxaTwo++;
}
numRead = input.read(current);
}
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalStateException("ReadDistanceMatrix: readBinMultiBlupCounts: Problem reading: " + filename);
}
}
}