Added a directory to house some Illumina output parsers. Hopefully this will be merged back into Picard at some point.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@126 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
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3e350006e0
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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//package edu.mit.broad.picard.illumina;
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package org.broadinstitute.sting.illumina;
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import edu.mit.broad.picard.util.BasicTextFileParser;
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import java.io.Closeable;
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import java.io.File;
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import java.io.FilenameFilter;
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import java.util.*;
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import net.sf.samtools.util.StringUtil;
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/**
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* Abstract base class for implementing parsers for various versions of Firecrest output
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*/
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public abstract class AbstractFirecrestFileParser implements Iterator<FirecrestReadData>, Iterable<FirecrestReadData>, Closeable {
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protected final int lane;
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protected final File firecrestDirectory;
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private FirecrestReadData next = null;
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private boolean iterating = false;
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/**
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* Examine the bustard directory to see if it is valid, and prepare for parsing
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*/
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public AbstractFirecrestFileParser(final File firecrestDirectory, final int lane) {
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this.lane = lane;
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this.firecrestDirectory = firecrestDirectory;
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}
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/**
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* @return true if the given bustard directory contains the appropriate files, or at least enough
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* of them so that it appears to be a Firecrest directory corresponding to the version of the concrete
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* FirecrestFileParser implementation.
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*/
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public abstract boolean isValidFirecrestDirectory();
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/**
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* Called before iteration begins. If this method is called when isValidFirecrestDirectory() had
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* return false, it will generate exceptions that may help the user diagnose the problem.
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*/
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protected abstract void prepareToIterate();
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/**
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* @return the next read
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*/
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protected abstract FirecrestReadData readNext();
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/**
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* @return an iterator over a set of elements of type FirecrestReadData
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*/
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public Iterator<FirecrestReadData> iterator() {
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if (iterating) {
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throw new IllegalStateException("iterator() method can only be called once, before the first call to hasNext()");
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}
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prepareToIterate();
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next = readNext();
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iterating = true;
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return this;
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}
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/**
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* @return true if the iteration has more elements. Otherwise returns false.
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*/
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public boolean hasNext() {
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if (!iterating) {
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iterator();
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}
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return next != null;
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}
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/**
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* Returns the next element in the iteration.
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*
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* @return the next element in the iteration
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* @throws java.util.NoSuchElementException
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*/
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public FirecrestReadData next() {
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if (!hasNext()) {
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throw new NoSuchElementException("Iteration has no more elements.");
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}
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final FirecrestReadData result = next;
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next = readNext();
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return result;
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}
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/**
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* Required method for Iterator API.
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*
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* @throws UnsupportedOperationException
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*/
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public void remove() {
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throw new UnsupportedOperationException("Remove() not supported.");
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}
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/**
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* Override, e.g. to close parser
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*/
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public void close() {
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}
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public int getLane() { return this.lane; }
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/**
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* Convenience method to create a parser for a list of files of the same format that should
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* be parsed in order defined by FirecrestFilenameComparator
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* @param files to be iterated, in arbitrary order
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* @return parser that iterates through the files in the appropriate order
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*/
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protected BasicTextFileParser makeParserForTextFiles(final boolean treatGroupedDelimitersAsOne, File[] files) {
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final SortedSet<File> sortedRead1 = new TreeSet<File>(new FirecrestFilenameComparator());
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sortedRead1.addAll(Arrays.asList(files));
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files = sortedRead1.toArray(files);
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return new BasicTextFileParser(treatGroupedDelimitersAsOne, files);
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}
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protected File[] getFilesMatchingRegexp(final String regexp) {
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return firecrestDirectory.listFiles( new FilenameFilter() {
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public boolean accept(final File dir, final String name) {
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return name.matches(regexp);
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}
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});
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}
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}
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package org.broadinstitute.sting.illumina;
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import edu.mit.broad.picard.util.PasteParser;
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import edu.mit.broad.picard.util.FormatUtil;
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import edu.mit.broad.picard.util.BasicTextFileParser;
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import edu.mit.broad.picard.PicardException;
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import java.io.File;
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/**
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* Class to parse the data in an Illumina Firecrest directory and return an iterator over that data, in order
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* by tile.
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*
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* @author Kiran Garimella
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*/
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public class FirecrestFileParser extends AbstractFirecrestFileParser {
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private BasicTextFileParser parser;
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private final FormatUtil formatter = new FormatUtil();
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private final File[] intensityFiles;
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/**
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* Constructor
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*
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* @param firecrestDirectory directory where the Firecrest files can be located
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* @param lane the lane to parse
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*/
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public FirecrestFileParser(final File firecrestDirectory, final int lane) {
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super(firecrestDirectory, lane);
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intensityFiles = getFilesMatchingRegexp("s_" + lane + "_\\d{4}_int.txt(.gz)?");
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}
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@Override
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public boolean isValidFirecrestDirectory() {
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return (intensityFiles.length > 0);
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}
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/**
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* Sorts the relevant files in the firecrestDirectory. Does some basic sanity checking to ensure that some files
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* are found and that they are the expected multiple for paired-end or not.
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*
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*/
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@Override
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protected void prepareToIterate() {
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// Some basic sanity checking on file counts
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if (intensityFiles.length == 0) {
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throw new PicardException("No Firecrest 1.3 intensity files found in " + firecrestDirectory.getAbsolutePath() + " for lane " + lane);
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}
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// Sort each set of reads and create a text parser for it
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parser = makeParserForTextFiles(true, intensityFiles);
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}
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/**
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* Parses the next line from the parser and constructs a FirecrestReadData object from it
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* The first 4 fields are position information for the read, and the remaining value are
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* the intensities data.
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*
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* @return a fully populated FirecrestReadData object
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*/
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protected FirecrestReadData readNext() {
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if (!parser.hasNext()) {
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return null;
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}
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final String[] data = parser.next();
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final int lane = formatter.parseInt(data[0]);
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final int tile = formatter.parseInt(data[1]);
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final int x = formatter.parseInt(data[2]);
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final int y = formatter.parseInt(data[3]);
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int intensityOffset = 4;
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int numIntensities = (data.length - 4)/4;
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FourIntensity[] intensities = new FourIntensity[numIntensities];
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for (int cycle = 0, index = intensityOffset; cycle < numIntensities; cycle++) {
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float[] fIntensities = new float[4];
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for (int channel = 0; channel < 4; channel++, index++) {
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fIntensities[channel] = formatter.parseFloat(data[index]);
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}
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intensities[cycle] = new FourIntensity(fIntensities);
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}
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return new FirecrestReadData(lane, tile, x, y, intensities);
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}
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/**
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* Closes the underlying PasteParser
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*/
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@Override
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public void close() {
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if (parser != null) {
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parser.close();
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}
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}
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}
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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//package edu.mit.broad.picard.illumina;
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package org.broadinstitute.sting.illumina;
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import java.io.File;
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import java.util.Comparator;
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/**
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* Comparator for getting Firecrest files in "sorted" order for use by the FirecrestFileParser. Expected order is
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* by lane in ascending order, then by tile in ascending order.
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*
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* IMPORTANT: Currently this class expects to receive ONLY int files.
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*
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* @author Kiran Garimella
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*/
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public class FirecrestFilenameComparator implements Comparator<File> {
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/**
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* Compares its two arguments for order. Returns a negative integer, zero, or a positive integer as
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* the first argument is less than, equal to, or greater than the second.
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*
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* @param file1
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* @param file2
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* @return a negative integer, zero, or a positive integer as
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* the first argument is less than, equal to, or greater than the second.
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*/
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public int compare(File file1, File file2)
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{
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Integer parts1[] = parseFileNameParts(file1.getName());
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Integer parts2[] = parseFileNameParts(file2.getName());
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for (int i = 1; i < parts1.length; i++)
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{
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if (!parts1[i].equals(parts2[i])) {
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return parts1[i].compareTo(parts2[i]);
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}
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}
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return 0;
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}
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/**
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* Utility method that returns an array of integers that represent, in order,
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* the lane, tile, type (0 for qseq files, 1 for sig2 files), and read (if any)
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* represented by the given file name
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*
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* @param name
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* @return an array of integers that represent, in order,
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* the lane, tile, type (0 for qseq files, 1 for sig2 files), and read (if any)
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* represented by the given file name
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*/
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private Integer[] parseFileNameParts(String name)
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{
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Integer parts[] = new Integer[3]; // Lane, tile, read
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String src[] = name.split("_");
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parts[0] = new Integer(src[1]); // Lane is always the second part
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if (src[2].length() == 4) { // Tile is 3rd or fourth
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parts[1] = new Integer(src[2]);
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}
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else {
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parts[1] = new Integer(src[3]);
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}
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if (src[2].length() == 1) { // read is last
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parts[2] = new Integer(src[2]);
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}
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return parts;
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}
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}
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package org.broadinstitute.sting.illumina;
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/**
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* Holds all the Firecrest-level data we need (so far) about an individual read.
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*
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* @author Kiran Garimella
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*/
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public class FirecrestReadData {
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final private int laneNumber;
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final private int tileNumber;
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final private int xCoordinate;
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final private int yCoordinate;
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final private FourIntensity[] intensities;
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/**
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* Constructor that takes everything to populate this object
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*
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* @param laneNumber
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* @param tileNumber
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* @param xCoordinate
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* @param yCoordinate
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* @param intensities
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*/
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public FirecrestReadData(int laneNumber, int tileNumber, int xCoordinate, int yCoordinate, FourIntensity[] intensities) {
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this.laneNumber = laneNumber;
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this.tileNumber = tileNumber;
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this.xCoordinate = xCoordinate;
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this.yCoordinate = yCoordinate;
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this.intensities = intensities;
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}
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/**
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* Composes a name for this read from its values.
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*
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* @return the read name
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*/
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public String getReadName() {
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return this.laneNumber + ":" + this.tileNumber + ":" + this.xCoordinate + ":" + this.yCoordinate + "#0";
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}
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public int getLaneNumber() { return laneNumber; }
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public int getTileNumber() { return tileNumber; }
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public int getXCoordinate() { return xCoordinate; }
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public int getYCoordinate() { return yCoordinate; }
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public FourIntensity[] getIntensities() { return intensities; }
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}
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package org.broadinstitute.sting.illumina;
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import java.util.StringTokenizer;
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public class FourIntensity {
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private float[] fIntensities;
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public FourIntensity() {
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fIntensities = new float[4];
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}
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public FourIntensity(float[] fIntensities) {
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this.fIntensities = fIntensities;
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}
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public FourIntensity(FourIntensity intensity) {
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fIntensities = new float[4];
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for (int channel = 0; channel < 4; channel++) {
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fIntensities[channel] = intensity.getChannelIntensity(channel);
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}
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}
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public void add(FourIntensity intensity) {
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for (int channel = 0; channel < 4; channel++) {
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fIntensities[channel] += intensity.getChannelIntensity(channel);
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}
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}
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public void subtract(FourIntensity intensity) {
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for (int channel = 0; channel < 4; channel++) {
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fIntensities[channel] -= intensity.getChannelIntensity(channel);
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}
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}
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public void divide(float divisor) {
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for (int channel = 0; channel < 4; channel++) {
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fIntensities[channel] /= divisor;
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}
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}
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public float getChannelIntensity(int channel) { return fIntensities[channel]; }
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public int brightestChannel() {
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int brightest = 0;
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for (int channel = 1; channel < 4; channel++) {
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if (fIntensities[channel] > fIntensities[brightest]) {
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brightest = channel;
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}
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}
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return brightest;
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}
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public String toString() {
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return "(" + getChannelIntensity(0) +
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", " + getChannelIntensity(1) +
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", " + getChannelIntensity(2) +
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", " + getChannelIntensity(3) +
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")";
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}
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}
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