net.maizegenetics.analysis.gbs.MergeMultipleTOPMPlugin Maven / Gradle / Ivy
/*
* MergeMultipleTOPMPlugin
*/
package net.maizegenetics.analysis.gbs;
import java.awt.Frame;
import java.io.BufferedInputStream;
import java.io.DataInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Arrays;
import javax.swing.ImageIcon;
import net.maizegenetics.dna.map.TOPMInterface;
import net.maizegenetics.dna.map.TOPMUtils;
import net.maizegenetics.plugindef.AbstractPlugin;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.util.ArgsEngine;
import net.maizegenetics.util.DirectoryCrawler;
import org.apache.log4j.Logger;
/**
*
* @author terry
*/
public class MergeMultipleTOPMPlugin extends AbstractPlugin {
private final Logger myLogger = Logger.getLogger(MergeMultipleTOPMPlugin.class);
private static String TOPM_FILENAME_REGEX = "(?i).*\\.topm$|.*\\.topm\\.bin";
private ArgsEngine myArgsEngine = null;
private String[] myTOPMFileNames = null;
private String myOutputFilename = null;
private String myOrigFilename = null;
private TOPMInterface myOrigTOPM = null;
private int myOrigTagCount = 0;
private byte[][] myOrigVariantOff = null;
private byte[][] myOrigVariantDef = null;
private boolean[] myChangedRows = null;
private int[] myChromosomeChangedCounts = new int[20];
public MergeMultipleTOPMPlugin(Frame parentFrame) {
super(parentFrame, false);
}
@Override
public DataSet performFunction(DataSet input) {
myOrigTOPM = TOPMUtils.readTOPM(myOrigFilename);
myOrigTagCount = myOrigTOPM.getTagCount();
myLogger.info("performFunction: Number of Original Tags: " + myOrigTagCount);
myOrigVariantOff = myOrigTOPM.getVariantOff();
myOrigVariantDef = myOrigTOPM.getVariantDef();
myChangedRows = new boolean[myOrigTagCount];
Arrays.fill(myChangedRows, false);
for (int i = 0; i < myTOPMFileNames.length; i++) {
if (!myTOPMFileNames[i].equals(myOrigFilename)) {
processTOPM(myTOPMFileNames[i]);
}
}
for (int x = 0; x < myChromosomeChangedCounts.length; x++) {
if (myChromosomeChangedCounts[x] != 0) {
myLogger.info("performFunction: chromosome: " + x + " changed: " + myChromosomeChangedCounts[x]);
}
}
TOPMUtils.writeTOPM(myOrigTOPM, myOutputFilename);
return null;
}
private void printUsage() {
myLogger.info(
"\nThe options for the MergeMultipleTOPMPlugin:\n"
+ "-input Input directory containing TOPM files\n"
+ "-orig Original TOPM\n"
+ "-result TOPM Output Filename\n");
}
@Override
public void setParameters(String[] args) {
if (args.length == 0) {
printUsage();
throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
}
if (myArgsEngine == null) {
myArgsEngine = new ArgsEngine();
myArgsEngine.add("-input", "-input", true);
myArgsEngine.add("-orig", "-orig", true);
myArgsEngine.add("-result", "-result", true);
}
myArgsEngine.parse(args);
String tempDirectory = myArgsEngine.getString("-input");
if ((tempDirectory != null) && tempDirectory.length() != 0) {
File topmDirectory = new File(tempDirectory);
if (!topmDirectory.isDirectory()) {
printUsage();
throw new IllegalArgumentException("MergeMultipleTOPMPlugin: setParameters: The input name you supplied is not a directory: " + tempDirectory);
}
myTOPMFileNames = DirectoryCrawler.listFileNames(TOPM_FILENAME_REGEX, topmDirectory.getAbsolutePath());
if (myTOPMFileNames.length == 0 || myTOPMFileNames == null) {
printUsage();
throw new IllegalArgumentException("MergeMultipleTOPMPlugin: setParameters: No TOPM files in: " + tempDirectory);
} else {
myLogger.info("setParameters: Using these TOPM files:");
for (String filename : myTOPMFileNames) {
myLogger.info(filename);
}
}
}
myOrigFilename = myArgsEngine.getString("-orig");
if ((myOrigFilename == null) || (myOrigFilename.length() == 0)) {
printUsage();
throw new IllegalArgumentException("MergeMultipleTOPMPlugin: setParameters: Must define original file");
}
File origFile = new File(myOrigFilename);
if (!origFile.exists()) {
printUsage();
throw new IllegalArgumentException("MergeMultipleTOPMPlugin: setParameters: The original file doesn't exist: " + myOrigFilename);
}
myOutputFilename = myArgsEngine.getString("-result");
if ((myOutputFilename == null) || (myOutputFilename.length() == 0)) {
printUsage();
throw new IllegalArgumentException("MergeMultipleTOPMPlugin: setParameters: Must define result file");
}
File outputFile = new File(myOutputFilename);
if (outputFile.exists()) {
printUsage();
throw new IllegalArgumentException("MergeMultipleTOPMPlugin: setParameters: The output file already exists: " + myOutputFilename);
}
}
private void processTOPM(String filename) {
myLogger.info("processTOPM: " + filename);
DataInputStream dis = null;
int tagsInput = 0;
try {
dis = new DataInputStream(new BufferedInputStream(new FileInputStream(filename), 65536));
int tagNum = dis.readInt();
int tagLengthInLong = dis.readInt();
int maxVariants = dis.readInt();
for (int row = 0; row < tagNum; row++) {
tagsInput++;
processTag(dis, row, tagLengthInLong, maxVariants);
if (row % 1000000 == 0) {
myLogger.info("processTOPM: Tags Read: " + row);
}
}
myLogger.info("processTOPM: Number of Tags: " + tagsInput);
} catch (Exception e) {
myLogger.error("processTOPM: Error Reading Tag: " + tagsInput);
e.printStackTrace();
throw new IllegalStateException("MergeMultipleTOPMPlugin: processTOPM: Problem processing: " + filename);
} finally {
try {
dis.close();
} catch (Exception e) {
// do nothing
}
}
}
private void processTag(DataInputStream dis, int row, int tagLengthInLong, int maxVariants) throws IOException {
long[] tags = new long[tagLengthInLong];
for (int j = 0; j < tagLengthInLong; j++) {
tags[j] = dis.readLong();
}
byte tagLength = dis.readByte();
byte multimaps = dis.readByte();
int chromosome = dis.readInt();
byte strand = dis.readByte();
int startPosition = dis.readInt();
int endPosition = dis.readInt();
byte divergence = dis.readByte();
byte[] variantPosOff = new byte[maxVariants];
byte[] variantDef = new byte[maxVariants];
for (int j = 0; j < maxVariants; j++) {
variantPosOff[j] = dis.readByte();
variantDef[j] = dis.readByte();
}
byte dcoP = dis.readByte();
byte mapP = dis.readByte();
if (myOrigTOPM.getTagLength(row) != tagLength) {
myLogger.error("processTag: " + row + " Tag Length: " + tagLength + " doesn't match Original: " + myOrigTOPM.getTagLength(row));
}
if (myOrigTOPM.getMultiMaps(row) != multimaps) {
myLogger.error("processTag: " + row + " Multi Maps: " + multimaps + " doesn't match Original: " + myOrigTOPM.getMultiMaps(row));
}
if (myOrigTOPM.getChromosome(row) != chromosome) {
myLogger.error("processTag: " + row + " Chromosome: " + chromosome + " doesn't match Original: " + myOrigTOPM.getChromosome(row));
}
if (myOrigTOPM.getStrand(row) != strand) {
myLogger.error("processTag: " + row + " Strand: " + strand + " doesn't match Original: " + myOrigTOPM.getStrand(row));
}
if (myOrigTOPM.getStartPosition(row) != startPosition) {
myLogger.error("processTag: " + row + " Start Position: " + startPosition + " doesn't match Original: " + myOrigTOPM.getStartPosition(row));
}
if (myOrigTOPM.getEndPosition(row) != endPosition) {
myLogger.error("processTag: " + row + " End Position: " + endPosition + " doesn't match Original: " + myOrigTOPM.getEndPosition(row));
}
if (myOrigTOPM.getDivergence(row) != divergence) {
myLogger.error("processTag: " + row + " Divergence: " + divergence + " doesn't match Original: " + myOrigTOPM.getDivergence(row));
}
if (myOrigTOPM.getDcoP(row) != dcoP) {
myLogger.error("processTag: " + row + " DcoP: " + dcoP + " doesn't match Original: " + myOrigTOPM.getDcoP(row));
}
if (myOrigTOPM.getMapP(row) != mapP) {
myLogger.error("processTag: " + row + " MapP: " + mapP + " doesn't match Original: " + myOrigTOPM.getMapP(row));
}
boolean variantsEqual = true;
for (int i = 0; i < maxVariants; i++) {
if (myOrigVariantDef[row][i] != variantDef[i]) {
variantsEqual = false;
break;
}
if (myOrigVariantOff[row][i] != variantPosOff[i]) {
variantsEqual = false;
break;
}
}
if (!variantsEqual) {
if (myChangedRows[row]) {
throw new IllegalStateException("MergeMultipleTOPMPlugin: processTag: " + row + " has already been merged.");
} else {
myChangedRows[row] = true;
if (chromosome < myChromosomeChangedCounts.length) {
myChromosomeChangedCounts[chromosome]++;
}
}
for (int i = 0; i < maxVariants; i++) {
myOrigTOPM.setVariantDef(row, i, variantDef[i]);
myOrigTOPM.setVariantPosOff(row, i, variantPosOff[i]);
}
}
}
@Override
public ImageIcon getIcon() {
return null;
}
@Override
public String getButtonName() {
throw new UnsupportedOperationException("Not supported yet.");
}
@Override
public String getToolTipText() {
throw new UnsupportedOperationException("Not supported yet.");
}
}
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