net.maizegenetics.analysis.gbs.KeepSpecifiedReadsinFastqPlugin Maven / Gradle / Ivy
/*
* KeepSpecifiedReadsinFastqPlugin
*/
package net.maizegenetics.analysis.gbs;
import java.awt.Frame;
import java.io.BufferedWriter;
import java.io.File;
import javax.swing.ImageIcon;
import net.maizegenetics.dna.map.TOPMInterface;
import net.maizegenetics.dna.map.TOPMUtils;
import net.maizegenetics.dna.tag.FastqReader;
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 KeepSpecifiedReadsinFastqPlugin extends AbstractPlugin {
private final Logger myLogger = Logger.getLogger(KeepSpecifiedReadsinFastqPlugin.class);
private static String FASTQ_FILENAME_REGEX = "(?i).*\\.fq$|.*\\.fq\\.gz$|.*\\.fastq$|.*_fastq\\.txt$|.*_fastq\\.gz$|.*_fastq\\.txt\\.gz$|.*_sequence\\.txt$|.*_sequence\\.txt\\.gz$";
private ArgsEngine myArgsEngine = null;
private String[] myInputFastqFileNames = null;
private String myOutputDir = null;
private String myTOPMFilename = null;
private String myKeyFilename = null;
private String myEnzyme = null;
private TOPMInterface myTOPM = null;
private int[] myChrs;
private int myStartPos;
private int myEndPos;
public KeepSpecifiedReadsinFastqPlugin(Frame parentFrame) {
super(parentFrame, false);
}
@Override
public DataSet performFunction(DataSet input) {
BufferedWriter writer = null;
try {
myTOPM = TOPMUtils.readTOPM(myTOPMFilename);
for (int i = 0; i < myInputFastqFileNames.length; i++) {
myLogger.info("Processing Fastq: " + myInputFastqFileNames[i]);
String outputFile = myOutputDir + "/" + Utils.getFilename(myInputFastqFileNames[i]);
myLogger.info("Output Fastq: " + outputFile);
writer = Utils.getBufferedWriter(outputFile);
ParseBarcodeRead thePBR = getParseBarcodeRead(myInputFastqFileNames[i]);
FastqReader reader = new FastqReader(myInputFastqFileNames[i]);
String[] current = reader.getNext();
while (current != null) {
ReadBarcodeResult rr = thePBR.parseReadIntoTagAndTaxa(current[1], current[3], true, 0);
if (rr != null) {
int index = myTOPM.getTagIndex(rr.getRead());
if (index >= 0) {
int chr = myTOPM.getChromosome(index);
int start = myTOPM.getStartPosition(index);
int end = myTOPM.getEndPosition(index);
if (isMatchingChr(chr)) {
if (((start >= myStartPos) && (start <= myEndPos))
|| ((end >= myStartPos) && (end <= myEndPos))) {
writer.write(current[0]);
writer.write("\n");
writer.write(current[1]);
writer.write("\n");
writer.write(current[2]);
writer.write("\n");
writer.write(current[3]);
writer.write("\n");
}
}
}
}
current = reader.getNext();
}
writer.close();
reader.close();
}
} catch (Exception e) {
e.printStackTrace();
} finally {
try {
writer.close();
} catch (Exception e) {
e.printStackTrace();
}
}
return null;
}
private void printUsage() {
myLogger.info(
"\nThe options for the KeepSpecifiedReadsinFastqPlugin:\n"
+ "-input Input directory containing fastq files\n"
+ "-topm TOPM\n"
+ "-k Key File\n"
+ "-e Enzyme\n"
+ "-output Output directory for resulting fastq files\n"
+ "-chrs Comma separated list of chromosomes. (no spaces)\n"
+ "-startPosition Start Position\n"
+ "-endPosition End Position\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("-topm", "-topm", true);
myArgsEngine.add("-k", "-k", true);
myArgsEngine.add("-e", "-e", true);
myArgsEngine.add("-output", "-output", true);
myArgsEngine.add("-chrs", "-chrs", true);
myArgsEngine.add("-startPosition", "-startPosition", true);
myArgsEngine.add("-endPosition", "-endPosition", true);
}
myArgsEngine.parse(args);
String tempDirectory = myArgsEngine.getString("-input");
if ((tempDirectory != null) && tempDirectory.length() != 0) {
File inputDirectory = new File(tempDirectory);
if (!inputDirectory.isDirectory()) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: The input name you supplied is not a directory: " + tempDirectory);
}
myInputFastqFileNames = DirectoryCrawler.listFileNames(FASTQ_FILENAME_REGEX, inputDirectory.getAbsolutePath());
if (myInputFastqFileNames.length == 0 || myInputFastqFileNames == null) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: No fastq files in: " + tempDirectory);
} else {
myLogger.info("setParameters: Using these fastq files:");
for (String filename : myInputFastqFileNames) {
myLogger.info("setParameters: found fastq: " + filename);
}
}
} else {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: No input directory specified.");
}
myTOPMFilename = myArgsEngine.getString("-topm");
if ((myTOPMFilename == null) || (myTOPMFilename.length() == 0)) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: Must define TOPM");
}
File tempFile = new File(myTOPMFilename);
if (!tempFile.exists()) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: The TOPM file doesn't exist: " + myTOPMFilename);
}
myKeyFilename = myArgsEngine.getString("-k");
if ((myKeyFilename == null) || (myKeyFilename.length() == 0)) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: Must define Key File");
}
tempFile = new File(myKeyFilename);
if (!tempFile.exists()) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: The Key file doesn't exist: " + myKeyFilename);
}
myEnzyme = myArgsEngine.getString("-e");
if ((myEnzyme == null) || (myEnzyme.length() == 0)) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: Must define TOPM");
}
myOutputDir = myArgsEngine.getString("-output");
if ((myOutputDir != null) && myOutputDir.length() != 0) {
File outputDirectory = new File(myOutputDir);
if (!outputDirectory.isDirectory()) {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: The output name you supplied is not a directory: " + myOutputDir);
}
} else {
printUsage();
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: No output directory specified.");
}
if (myOutputDir.equals(tempDirectory)) {
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: Output Directory should be different from Input Directory");
}
String tempChrs = myArgsEngine.getString("-chrs");
if ((tempChrs == null) || tempChrs.length() == 0) {
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: No chromosomes specified.");
}
String[] tokenChrs = tempChrs.split(",");
myChrs = new int[tokenChrs.length];
for (int i = 0; i < tokenChrs.length; i++) {
try {
myChrs[i] = Integer.parseInt(tokenChrs[i]);
} catch (NumberFormatException e) {
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: chromosome not a number: " + tokenChrs[i]);
}
}
String tempStart = myArgsEngine.getString("-startPosition");
if ((tempStart == null) || tempStart.length() == 0) {
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: No Start Position specified.");
}
try {
myStartPos = Integer.parseInt(tempStart);
} catch (NumberFormatException e) {
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: Start Position not a number: " + tempStart);
}
String tempEnd = myArgsEngine.getString("-endPosition");
if ((tempEnd == null) || tempEnd.length() == 0) {
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: No End Position specified.");
}
try {
myEndPos = Integer.parseInt(tempEnd);
} catch (NumberFormatException e) {
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: End Position not a number: " + tempEnd);
}
if (myStartPos > myEndPos) {
throw new IllegalArgumentException("KeepSpecifiedReadsinFastqPlugin: setParameters: Start Position: " + myStartPos + " can't be larger than End Position: " + myEndPos);
}
}
private boolean isMatchingChr(int chr) {
for (int i = 0; i < myChrs.length; i++) {
if (myChrs[i] == chr) {
return true;
}
}
return false;
}
private ParseBarcodeRead getParseBarcodeRead(String fastqFile) {
String[] np = Utils.getFilename(fastqFile).split("_");
ParseBarcodeRead result;
if (np.length == 3) {
result = new ParseBarcodeRead(myKeyFilename, myEnzyme, np[0], np[1]);
} else if (np.length == 5) {
result = new ParseBarcodeRead(myKeyFilename, myEnzyme, np[1], np[3]);
} else if (np.length == 4) {
result = new ParseBarcodeRead(myKeyFilename, myEnzyme, np[0], np[2]);
} else if (np.length == 6) {
result = new ParseBarcodeRead(myKeyFilename, myEnzyme, np[1], np[3]);
} else {
myLogger.error("Error in parsing file name:");
myLogger.error(" The filename does not contain either 3 or 5 underscore-delimited values.");
myLogger.error(" Expect: flowcell_lane_fastq.txt OR code_flowcell_s_lane_fastq.txt");
myLogger.error(" Filename: " + fastqFile);
return null;
}
myLogger.info("Total barcodes found in lane:" + result.getBarCodeCount());
return result;
}
@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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