net.maizegenetics.analysis.gbs.KeepSpecifiedSitesInTOPMPlugin Maven / Gradle / Ivy
/*
* KeepSpecifiedSitesInTOPMPlugin
*/
package net.maizegenetics.analysis.gbs;
import java.awt.Frame;
import java.io.BufferedReader;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.regex.Pattern;
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 net.maizegenetics.util.Utils;
import org.apache.log4j.Logger;
/**
*
* @author terry
*/
public class KeepSpecifiedSitesInTOPMPlugin extends AbstractPlugin {
private static final Pattern WHITESPACE_PATTERN = Pattern.compile("\\s");
private final Logger myLogger = Logger.getLogger(KeepSpecifiedSitesInTOPMPlugin.class);
private static String SITE_LIST_FILENAME_REGEX = "(?i).*\\.txt$";
private static int PAD_POSITION = 300;
private ArgsEngine myArgsEngine = null;
private String[] mySiteListFileNames = 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 int[] myNumVariantsKeptPerChrom = new int[20];
private int[] myTagsWithVariants = new int[20];
public KeepSpecifiedSitesInTOPMPlugin(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();
myOrigTOPM.clearVariants();
for (int i = 0; i < mySiteListFileNames.length; i++) {
if (!mySiteListFileNames[i].equals(myOrigFilename)) {
processSiteList(mySiteListFileNames[i]);
}
}
for (int x = 0; x < myNumVariantsKeptPerChrom.length; x++) {
if (myNumVariantsKeptPerChrom[x] != 0) {
myLogger.info("performFunction: chromosome: " + x + " variants kept: " + myNumVariantsKeptPerChrom[x]);
}
}
for (int x = 0; x < myTagsWithVariants.length; x++) {
if (myTagsWithVariants[x] != 0) {
myLogger.info("performFunction: Chromosome: " + x + " Number Tags with Variants Defined: " + myTagsWithVariants[x]);
}
}
TOPMUtils.writeTOPM(myOrigTOPM, myOutputFilename);
return null;
}
private void printUsage() {
myLogger.info(
"\n\n\nThe options for the KeepSpecifiedSitesInTOPMPlugin are:\n"
+ " -input Input directory containing Site List files\n"
+ " -orig Original TOPM\n"
+ " -result Output, site-filtered TOPM\n\n\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("KeepSpecifiedSitesInTOPMPlugin: setParameters: The input name you supplied is not a directory: " + tempDirectory);
}
mySiteListFileNames = DirectoryCrawler.listFileNames(SITE_LIST_FILENAME_REGEX, topmDirectory.getAbsolutePath());
if (mySiteListFileNames.length == 0 || mySiteListFileNames == null) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedSitesInTOPMPlugin: setParameters: No Site List files in: " + tempDirectory);
} else {
myLogger.info("setParameters: Using these Site List files:");
for (String filename : mySiteListFileNames) {
myLogger.info("setParameters: found site list: " + filename);
}
}
}
myOrigFilename = myArgsEngine.getString("-orig");
if ((myOrigFilename == null) || (myOrigFilename.length() == 0)) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedSitesInTOPMPlugin: setParameters: Must define original file");
}
File origFile = new File(myOrigFilename);
if (!origFile.exists()) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedSitesInTOPMPlugin: setParameters: The original file doesn't exist: " + myOrigFilename);
}
myOutputFilename = myArgsEngine.getString("-result");
if ((myOutputFilename == null) || (myOutputFilename.length() == 0)) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedSitesInTOPMPlugin: setParameters: Must define result file");
}
File outputFile = new File(myOutputFilename);
if (outputFile.exists()) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedSitesInTOPMPlugin: setParameters: The output file already exists: " + myOutputFilename);
}
}
private void processSiteList(String filename) {
myLogger.info("processSiteList: " + filename);
BufferedReader reader = Utils.getBufferedReader(filename);
try {
List positions = new ArrayList();
String line = reader.readLine();
String chr = WHITESPACE_PATTERN.split(line)[0];
while (line != null) {
String[] tokens = WHITESPACE_PATTERN.split(line);
if (tokens.length != 2) {
throw new IllegalArgumentException("KeepSpecifiedSitesInTOPMPlugin: processSiteList: file not correctly formatted: " + filename);
}
if (!tokens[0].equals(chr)) {
throw new IllegalArgumentException("KeepSpecifiedSitesInTOPMPlugin: processSiteList: all positions must be from same chromosome: " + filename);
}
positions.add(Integer.valueOf(tokens[1]));
line = reader.readLine();
}
reader.close();
int numPositions = positions.size();
int[] orderedPositions = new int[numPositions];
for (int j = 0; j < numPositions; j++) {
orderedPositions[j] = positions.get(j);
}
Arrays.sort(orderedPositions);
int[] numTagsWithUnfoundSitesAndMaxVariants = new int[numPositions];
int numVariants = myOrigVariantOff[0].length;
int chrInt = Integer.valueOf(chr);
int tagCount = myOrigTOPM.getTagCount();
for (int i = 0; i < tagCount; i++) {
if (myOrigTOPM.getChromosome(i) == chrInt) {
int startPos = myOrigTOPM.getStartPosition(i);
int endPos = myOrigTOPM.getEndPosition(i);
byte strand = myOrigTOPM.getStrand(i);
if (strand == -1) {
if (endPos > startPos) {
throw new IllegalStateException("KeepSpecifiedSitesInTOPMPlugin: processSiteList: tag: " + i + " strand: " + strand + " end pos: " + endPos + " is greater than start pos: " + startPos);
}
int posIndex = Arrays.binarySearch(orderedPositions, Math.max(endPos - PAD_POSITION, 0));
if (posIndex < 0) {
posIndex = -(posIndex + 1);
}
int variantAdded = 0;
while ((posIndex < numPositions) && (orderedPositions[posIndex] <= startPos + PAD_POSITION)) {
boolean found = false;
int currentPosition = orderedPositions[posIndex];
for (int x = 0; x < numVariants; x++) {
if ((myOrigVariantOff[i][x] != Byte.MIN_VALUE) && (myOrigVariantDef[i][x] != Byte.MIN_VALUE)) {
int tagPosition = myOrigVariantOff[i][x] + startPos;
if (tagPosition == currentPosition) {
found = true;
myOrigTOPM.addVariant(i, myOrigVariantOff[i][x], myOrigVariantDef[i][x]);
variantAdded = 1;
if (chrInt < myNumVariantsKeptPerChrom.length) {
myNumVariantsKeptPerChrom[chrInt]++;
}
}
}
}
if (found) {
numTagsWithUnfoundSitesAndMaxVariants[posIndex] = -1;
} else if ((!found) && (numVariants == myOrigTOPM.getMaxNumVariants()) && (numTagsWithUnfoundSitesAndMaxVariants[posIndex] != -1)
&& (currentPosition <= startPos) && (currentPosition >= endPos)) {
numTagsWithUnfoundSitesAndMaxVariants[posIndex]++;
}
posIndex++;
}
myTagsWithVariants[chrInt] += variantAdded;
} else if (strand == 1) {
if (startPos > endPos) {
throw new IllegalStateException("KeepSpecifiedSitesInTOPMPlugin: processSiteList: tag: " + i + " strand: " + strand + " start pos: " + startPos + " is greater than end pos: " + endPos);
}
int posIndex = Arrays.binarySearch(orderedPositions, Math.max(startPos - PAD_POSITION, 0));
if (posIndex < 0) {
posIndex = -(posIndex + 1);
}
int variantAdded = 0;
while ((posIndex < numPositions) && (orderedPositions[posIndex] <= endPos + PAD_POSITION)) {
boolean found = false;
int currentPosition = orderedPositions[posIndex];
for (int x = 0; x < numVariants; x++) {
if ((myOrigVariantOff[i][x] != Byte.MIN_VALUE) && (myOrigVariantDef[i][x] != Byte.MIN_VALUE)) {
int tagPosition = myOrigVariantOff[i][x] + startPos;
if (tagPosition == currentPosition) {
found = true;
myOrigTOPM.addVariant(i, myOrigVariantOff[i][x], myOrigVariantDef[i][x]);
variantAdded = 1;
if (chrInt < myNumVariantsKeptPerChrom.length) {
myNumVariantsKeptPerChrom[chrInt]++;
}
}
}
}
if (found) {
numTagsWithUnfoundSitesAndMaxVariants[posIndex] = -1;
} else if ((!found) && (numVariants == myOrigTOPM.getMaxNumVariants()) && (numTagsWithUnfoundSitesAndMaxVariants[posIndex] != -1)
&& (currentPosition >= startPos) && (currentPosition <= endPos)) {
numTagsWithUnfoundSitesAndMaxVariants[posIndex]++;
}
posIndex++;
}
myTagsWithVariants[chrInt] += variantAdded;
} else {
throw new IllegalStateException("KeepSpecifiedSitesInTOPMPlugin: processSiteList: tag: " + i + " unknown strand: " + strand);
}
}
}
for (int i = 0; i < numPositions; i++) {
if (numTagsWithUnfoundSitesAndMaxVariants[i] > 0) {
myLogger.info("chromosome: " + chrInt + " position: " + orderedPositions[i] + " tags with no variant info: " + numTagsWithUnfoundSitesAndMaxVariants[i]);
}
}
} catch (Exception e) {
e.printStackTrace();
throw new IllegalStateException("KeepSpecifiedSitesInTOPMPlugin: processSiteList: Problem processing: " + filename);
} finally {
try {
reader.close();
} catch (Exception e) {
// do nothing
}
}
}
@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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