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net.maizegenetics.analysis.gbs.pana.PanAReadToKmerPlugin Maven / Gradle / Ivy
package net.maizegenetics.analysis.gbs.pana;
import net.maizegenetics.plugindef.AbstractPlugin;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.util.ArgsEngine;
import net.maizegenetics.util.DirectoryCrawler;
import net.maizegenetics.util.MultiMemberGZIPInputStream;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import javax.swing.*;
import java.awt.*;
import java.io.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.TreeSet;
import net.maizegenetics.dna.BaseEncoder;
import net.maizegenetics.dna.tag.TagCountMutable;
import net.maizegenetics.dna.tag.TagCounts;
import net.maizegenetics.dna.tag.TagsByTaxa;
import net.maizegenetics.dna.tag.TagsByTaxa.FilePacking;
import net.maizegenetics.dna.tag.UTagCountMutable;
/**
* Generate Kmers from Fastq/Qseq data
* Do not use underscore in taxa name in keyfile
* @author Fei Lu
*/
public class PanAReadToKmerPlugin extends AbstractPlugin {
static long timePoint1;
private ArgsEngine engine = null;
private Logger logger = LogManager.getLogger(PanAReadToKmerPlugin.class);
String polyA = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA";
//user definable parameters
String rawSeqDirS = null;
String keyFileS = null;
int customTagLength = 0;
String outDirS = null;
int inputFormatValue;
//calculatable parameters
int tagLengthInLong;
String[] lanes = null;
HashMap laneTaxaMap = null;
public PanAReadToKmerPlugin() {
super(null, false);
}
public PanAReadToKmerPlugin(Frame parentFrame) {
super(parentFrame, false);
}
private void printUsage() {
logger.info(
"\n\nUsage is as follows:\n"
+ " -i input directory of Fastq or Qseq files\n"
+ " -f input format value. 0 = Fastq. 1 = Qseq\n"
+ " -k key file which links Fastq/Qseq file with samples\n"
+ " -l customed tag length\n"
+ " -o output directory of tag count files\n");
}
@Override
public DataSet performFunction(DataSet input) {
this.getLaneTaxaInfo();
if (this.inputFormatValue == 0) {
this.processFastq();
}
else if (this.inputFormatValue == 1) {
this.processQseq();
}
else {
}
this.mergeTagCounts();
return null;
}
private void mergeTagCounts () {
File[] tcFiles = new File (outDirS).listFiles(new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
return name.toLowerCase().endsWith("cnt");
}
});
Arrays.sort(tcFiles);
TreeSet taxaNameSet = new TreeSet();
for (int i = 0; i < tcFiles.length; i++) {
String[] temp = tcFiles[i].getName().substring(0, tcFiles[i].getName().length()-4).split("_");
String theTaxon = temp[temp.length-1];
taxaNameSet.add(theTaxon);
}
String[] taxaNames = taxaNameSet.toArray(new String[taxaNameSet.size()]);
for (int i = 0; i < taxaNames.length; i++) {
System.out.println("Merging tagCount files for taxa " + taxaNames[i]);
ArrayList fileList = new ArrayList();
for (int j = 0; j < tcFiles.length; j++) {
String[] temp = tcFiles[j].getName().substring(0, tcFiles[j].getName().length()-4).split("_");
String theTaxon = temp[temp.length-1];
if (taxaNames[i].equals(theTaxon)) fileList.add(tcFiles[j]);
}
if (fileList.size() == 1) {
File dest = new File(fileList.get(0).getParent(), taxaNames[i]+".cnt");
fileList.get(0).renameTo(dest);
System.out.println("File is renamed to " + dest.getAbsolutePath());
}
else if (fileList.size() > 1){
File dest = new File(fileList.get(0).getParent(), taxaNames[i]+".cnt");
UTagCountMutable tcu = new UTagCountMutable(this.tagLengthInLong, 0);
for (int j = 0; j < fileList.size(); j++) {
TagCounts tc = new TagCounts(fileList.get(j).getAbsolutePath(), FilePacking.Byte);
for (int k = 0; k < tc.getTagCount(); k++) {
long[] t = tc.getTag(k);
tcu.addReadCount(t, tc.getTagLength(k), tc.getReadCount(k));
}
}
tcu.toArray();
tcu.collapseCounts();
tcu.writeTagCountFile(dest.getAbsolutePath(), FilePacking.Byte, 1);
for (int j = 0; j < fileList.size(); j++) {
fileList.get(j).delete();
}
System.out.println(String.valueOf(fileList.size()) + " files are merged into " + dest.getAbsolutePath());
}
System.out.println();
}
}
private void processFastq () {
BufferedReader br;
for (int i = 0; i < lanes.length; i++) {
File infile = new File(rawSeqDirS, lanes[i]);
if (!infile.exists()) {
System.out.println(infile.getAbsolutePath() + " doesn't exist. Program stops");
System.exit(1);
}
String infileS = infile.getAbsolutePath();
try {
String outfileS = new File (this.outDirS,lanes[i]+"_"+laneTaxaMap.get(lanes[i])+".cnt").getAbsolutePath();
if (infileS.endsWith(".gz")) {
br = new BufferedReader(new InputStreamReader(new MultiMemberGZIPInputStream(new FileInputStream(infile))));
}
else {
br = new BufferedReader(new FileReader(infile), 65536);
}
System.out.println("Start reading " + infile.getAbsolutePath());
String temp = br.readLine();
temp = br.readLine();
System.out.println("Sequence length is " + temp.length() + " bps in file " + infileS);
int actualLength = temp.length();
if (temp.length() < this.customTagLength) {
System.out.println("Custom tag length is longer than actual sequence length in file. Programs stops");
System.exit(0);
}
br.readLine();
br.readLine();
//int numKmersLine = actualLength-this.customTagLength+1;
int numKmersLine = 1;
UTagCountMutable tcu = new UTagCountMutable(this.tagLengthInLong, 0);
String tag = null;
long[] t;
long tagCnt = 0;
while ((temp = br.readLine()) != null) {
temp = br.readLine();
for (int j = 0; j < numKmersLine; j++) {
tag = temp.substring(j, j+this.customTagLength);
if (!this.isBadSequence(tag)) {
t = BaseEncoder.getLongArrayFromSeq(tag);
tcu.addReadCount(t, this.customTagLength, 1);
tagCnt++;
}
}
br.readLine();
br.readLine();
}
br.close();
tcu.toArray();
tcu.collapseCounts();
tcu.writeTagCountFile(outfileS, TagsByTaxa.FilePacking.Byte, 1);
System.out.println("Generated " + String.valueOf(tagCnt)+ " Kmers/tags from " + infile.getAbsolutePath());
System.out.println();
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
private void processQseq () {
BufferedReader br;
for (int i = 0; i < lanes.length; i++) {
File infile = new File(rawSeqDirS, lanes[i]);
if (!infile.exists()) {
System.out.println(infile.getAbsolutePath() + " doesn't exist. Program stops");
System.exit(1);
}
String infileS = infile.getAbsolutePath();
try {
String outfileS = new File (this.outDirS,lanes[i]+"_"+laneTaxaMap.get(lanes[i])+".cnt").getAbsolutePath();
if (infileS.endsWith(".gz")) {
br = new BufferedReader(new InputStreamReader(new MultiMemberGZIPInputStream(new FileInputStream(infile))));
}
else {
br = new BufferedReader(new FileReader(infile), 65536);
}
System.out.println("Start reading " + infile.getAbsolutePath());
String temp = br.readLine();
String[] tem = temp.split("\t");
System.out.println("Sequence length is " + tem[8].length() + " bps in file " + infileS);
int actualLength = tem[8].length();
if (tem[8].length() < this.customTagLength) {
System.out.println("Custom tag length is longer than actual sequence length in file. Programs stops");
System.exit(0);
}
//int numKmersLine = actualLength-this.customTagLength+1;
int numKmersLine = 1;
UTagCountMutable tcu = new UTagCountMutable(this.tagLengthInLong, 0);
String tag = null;
long[] t;
long tagCnt = 0;
while ((temp = br.readLine()) != null) {
for (int j = 0; j < numKmersLine; j++) {
tag = temp.substring(j, j+this.customTagLength);
if (!this.isBadSequence(tag)) {
t = BaseEncoder.getLongArrayFromSeq(tag);
tcu.addReadCount(t, this.customTagLength, 1);
tagCnt++;
}
}
}
br.close();
tcu.toArray();
tcu.collapseCounts();
tcu.writeTagCountFile(outfileS, TagsByTaxa.FilePacking.Byte, 1);
System.out.println("Generated " + String.valueOf(tagCnt)+ " Kmers/tags from " + infile.getAbsolutePath());
System.out.println();
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
}
private boolean isBadSequence (String seq) {
if (seq.indexOf("N") != -1) return true;
if (seq.indexOf(".") != -1) return true;
return false;
}
private void getLaneTaxaInfo () {
laneTaxaMap = new HashMap();
ArrayList laneList =new ArrayList();
try {
BufferedReader br = new BufferedReader(new FileReader(keyFileS), 65536);
String temp = br.readLine();
while ((temp = br.readLine())!=null) {
String[] tem = temp.split("\t");
laneList.add(tem[0]);
laneTaxaMap.put(tem[0], tem[1]);
}
}
catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
lanes = laneList.toArray(new String[laneList.size()]);
}
@Override
public void setParameters(String[] args) {
if (args.length == 0) {
printUsage();
throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
}
if (engine == null) {
engine = new ArgsEngine();
engine.add("-i", "--input-DirS", true);
engine.add("-f", "--input-format", true);
engine.add("-k", "--key-file", true);
engine.add("-l", "--costum-tagLength", true);
engine.add("-o", "--output-DirS", true);
engine.parse(args);
}
if (engine.getBoolean("-i")) {
rawSeqDirS = engine.getString("-i");
}
else {
printUsage();
throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
}
if (engine.getBoolean("-f")) {
this.inputFormatValue = Integer.valueOf(engine.getString("-f"));
if (this.inputFormatValue != 0 && this.inputFormatValue != 1) {
printUsage();
throw new IllegalArgumentException("\n\nPlease double input format value.\n\n");
}
}
else {
printUsage();
throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
}
if (engine.getBoolean("-k")) {
keyFileS = engine.getString("-k");
}
else {
printUsage();
throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
}
if (engine.getBoolean("-l")) {
customTagLength = Integer.valueOf(engine.getString("-l"));
int base = customTagLength%BaseEncoder.chunkSize;
if (base == 0) {
this.tagLengthInLong = customTagLength/BaseEncoder.chunkSize;
}
else {
this.tagLengthInLong = customTagLength/BaseEncoder.chunkSize+1;
}
}
else {
printUsage();
throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
}
if (engine.getBoolean("-o")) {
outDirS = engine.getString("-o");
}
else {
printUsage();
throw new IllegalArgumentException("\n\nPlease use the above arguments/options.\n\n");
}
}
@Override
public ImageIcon getIcon() {
throw new UnsupportedOperationException("Not supported yet.");
}
@Override
public String getButtonName() {
throw new UnsupportedOperationException("Not supported yet.");
}
@Override
public String getToolTipText() {
throw new UnsupportedOperationException("Not supported yet.");
}
}
