Refactored into oblivon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@276 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
dffc879240
commit
7d889c0661
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@ -1,243 +0,0 @@
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package org.broadinstitute.sting.playground.fourbasecaller;
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import java.io.File;
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import java.util.Vector;
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import java.lang.Math;
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import org.broadinstitute.sting.playground.illumina.FirecrestFileParser;
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import org.broadinstitute.sting.playground.illumina.FourIntensity;
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import cern.colt.matrix.linalg.Algebra;
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import cern.colt.matrix.DoubleMatrix1D;
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import cern.colt.matrix.DoubleFactory1D;
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import net.sf.samtools.SAMFileHeader;
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import net.sf.samtools.SAMFileWriter;
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import net.sf.samtools.SAMFileWriterFactory;
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import net.sf.samtools.SAMRecord;
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public class FourBaseCaller {
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public static void main(String[] argv) {
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// Parse args
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File FIRECREST_DIR = new File(argv[0]);
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int LANE = Integer.valueOf(argv[1]);
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File SAM_OUT = new File(argv[2]);
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int CYCLE_START = Integer.valueOf(argv[3]);
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int CYCLE_STOP = Integer.valueOf(argv[4]);
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String IC_REF_PATH = "/seq/references/Synthetic_internal_controls_set1/v0/Synthetic_internal_controls_set1.fasta";
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// Load ic reference in an ugly way
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ManyNucleotideSequences fw_controls = new ManyNucleotideSequences(IC_REF_PATH);
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ManyNucleotideSequences rc_controls = new ManyNucleotideSequences(IC_REF_PATH);
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rc_controls.reverseComplement();
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ManyNucleotideSequences controls = new ManyNucleotideSequences();
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controls.addAll(fw_controls);
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controls.addAll(rc_controls);
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// Loop through firecrest data, find ICs, and compute signal means
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Vector<FourIntensity[]> recoveredICs = new Vector<FourIntensity[]>();
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Vector<Integer> icids = new Vector<Integer>();
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FirecrestFileParser ffp = new FirecrestFileParser(FIRECREST_DIR, LANE, CYCLE_START, CYCLE_STOP);
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NucleotideChannelMeans[] cmeans = new NucleotideChannelMeans[controls.get(0).size()];
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for (int i = 0; i < cmeans.length; i++) {
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cmeans[i] = new NucleotideChannelMeans();
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}
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int numReads = 0;
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while (ffp.hasNext()) {
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if (numReads % 1000000 == 0) {
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System.err.println("Processed " + numReads + " reads for parameters.");
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}
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FourIntensity[] intensities = ffp.next().getIntensities();
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NucleotideSequence rawread = toNucleotideSequence(intensities);
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int[] editDistances = new int[controls.size()];
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for (int icTemplateIndex = 0; icTemplateIndex < controls.size(); icTemplateIndex++) {
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editDistances[icTemplateIndex] = rawread.editDistance(controls.get(icTemplateIndex), 36);
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if (editDistances[icTemplateIndex] <= 8) {
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recoveredICs.add(intensities);
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icids.add(icTemplateIndex);
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for (int cycle = 0; cycle < ((controls.get(0).size() < intensities.length) ? controls.get(0).size() : intensities.length); cycle++) {
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Nucleotide nuc = controls.get(icTemplateIndex).get(cycle);
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FourIntensity sig = intensities[cycle];
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cmeans[cycle].add(nuc, sig);
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}
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System.err.print("Found " + icids.size() + " ICs in " + numReads + " reads " + (((double) icids.size())/((double) numReads)) + ".\r");
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break;
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}
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}
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numReads++;
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}
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// Go through the data again and compute signal covariances
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NucleotideChannelCovariances[] ccov = new NucleotideChannelCovariances[controls.get(0).size()];
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for (int i = 0; i < cmeans.length; i++) {
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ccov[i] = new NucleotideChannelCovariances();
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}
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for (int index = 0; index < recoveredICs.size(); index++) {
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NucleotideSequence control = controls.get(icids.get(index).intValue());
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FourIntensity[] intensities = recoveredICs.get(index);
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int seqlength = (control.size() < intensities.length) ? control.size() : intensities.length;
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for (int cycle = 0; cycle < seqlength; cycle++) {
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Nucleotide nuc = control.get(cycle);
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FourIntensity sig = intensities[cycle];
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NucleotideChannelMeans mus = cmeans[cycle];
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ccov[cycle].add(nuc, sig, mus);
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}
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}
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System.out.println("Found " + recoveredICs.size() + " in " + numReads + " reads.");
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// Extend IC solutions to end of read length (if ICs are shorter than read)
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System.err.println("Extending cycle " + (controls.get(0).size() - 1) + " parameters from cycle " + controls.get(0).size() + " to cycle " + recoveredICs.get(0).length);
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for (int cycle = controls.get(0).size(); cycle < recoveredICs.get(0).length; cycle++) {
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cmeans[cycle] = cmeans[controls.get(0).size() - 1];
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ccov[cycle] = ccov[controls.get(0).size() - 1];
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}
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// Now compute probabilities for the bases
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Algebra alg = new Algebra();
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for (int cycle = 0; cycle < recoveredICs.get(0).length; cycle++) {
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ccov[cycle].invert();
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}
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FirecrestFileParser ffp2 = new FirecrestFileParser(FIRECREST_DIR, LANE, CYCLE_START, CYCLE_STOP);
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SAMFileHeader sfh = new SAMFileHeader();
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SAMFileWriter sfw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sfh, false, SAM_OUT);
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numReads = 0;
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while (ffp2.hasNext()) {
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if (numReads % 1000000 == 0) {
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System.err.println("Basecalled " + numReads + " reads.");
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}
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FourIntensity[] intensities = ffp2.next().getIntensities();
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byte[] asciiseq = new byte[intensities.length];
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byte[] bestqual = new byte[intensities.length];
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byte[] nextbestqual = new byte[intensities.length];
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for (int cycle = 0; cycle < intensities.length; cycle++) {
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FourIntensity fi = intensities[cycle];
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double[] likes = new double[4];
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double total = 0.0;
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for (Nucleotide nuc : Nucleotide.values()) {
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double norm = Math.sqrt(alg.det(ccov[cycle].channelCovariances(nuc)))/Math.pow(2.0*Math.PI, 2.0);
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DoubleMatrix1D sub = subtract(fi, cmeans[cycle].channelMeans(nuc));
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DoubleMatrix1D Ax = alg.mult(ccov[cycle].channelCovariances(nuc), sub);
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double exparg = -0.5*alg.mult(sub, Ax);
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likes[nuc.ordinal()] = norm*Math.exp(exparg);
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total += likes[nuc.ordinal()];
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}
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Nucleotide call1 = Nucleotide.A;
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double prob1 = likes[0]/total;
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for (int i = 1; i < 4; i++) {
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if (likes[i]/total > prob1) {
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prob1 = likes[i]/total;
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switch (i) {
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case 1: call1 = Nucleotide.C; break;
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case 2: call1 = Nucleotide.G; break;
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case 3: call1 = Nucleotide.T; break;
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}
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}
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}
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Nucleotide call2 = Nucleotide.A;
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double prob2 = 0.0;
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for (int i = 0; i < 4; i++) {
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if (i != call1.ordinal() && likes[i]/total > prob2 && likes[i]/total < prob1) {
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prob2 = likes[i]/total;
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switch (i) {
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case 0: call2 = Nucleotide.A; break;
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case 1: call2 = Nucleotide.C; break;
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case 2: call2 = Nucleotide.G; break;
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case 3: call2 = Nucleotide.T; break;
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}
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}
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}
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asciiseq[cycle] = (byte) call1.asChar();
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bestqual[cycle] = toPhredScore(prob1);
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nextbestqual[cycle] = toCompressedQuality(call2, prob2);
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}
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SAMRecord sr = new SAMRecord(sfh);
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sr.setReadName(Integer.toString(numReads));
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sr.setReadUmappedFlag(true);
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sr.setReadBases(asciiseq);
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sr.setBaseQualities(bestqual);
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sr.setAttribute("SQ", nextbestqual);
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sfw.addAlignment(sr);
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numReads++;
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}
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sfw.close();
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System.out.println("Done.");
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}
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private static byte toPhredScore(double prob) {
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byte qual = (1.0 - prob < 0.00001) ? 40 : (byte) (-10*Math.log10(1.0 - prob));
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return (qual > 40) ? 40 : qual;
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}
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private static DoubleMatrix1D subtract(FourIntensity a, FourIntensity b) {
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DoubleMatrix1D sub = (DoubleFactory1D.dense).make(4);
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for (int i = 0; i < 4; i++) {
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sub.set(i, a.getChannelIntensity(i) - b.getChannelIntensity(i));
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}
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return sub;
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}
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private static byte toCompressedQuality(Nucleotide base, double prob) {
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byte compressedQual = (byte) base.ordinal();
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byte cprob = (byte) (100.0*prob);
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byte qualmask = (byte) 252;
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compressedQual += ((cprob << 2) & qualmask);
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return compressedQual;
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}
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private static NucleotideSequence toNucleotideSequence(FourIntensity[] intensities) {
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NucleotideSequence ns = new NucleotideSequence(intensities.length);
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for (int cycle = 0; cycle < intensities.length; cycle++) {
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int brightestChannel = intensities[cycle].brightestChannel();
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Nucleotide nt = Nucleotide.A;
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switch (brightestChannel) {
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case 0: nt = Nucleotide.A; break;
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case 1: nt = Nucleotide.C; break;
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case 2: nt = Nucleotide.G; break;
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case 3: nt = Nucleotide.T; break;
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}
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ns.set(cycle, nt);
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}
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return ns;
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}
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}
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package org.broadinstitute.sting.playground.fourbasecaller;
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import java.io.File;
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import java.util.Vector;
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import org.broadinstitute.sting.playground.fourbasecaller.NucleotideSequence;
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import edu.mit.broad.picard.reference.ReferenceSequence;
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import edu.mit.broad.picard.reference.ReferenceSequenceFile;
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import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
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class ManyNucleotideSequences extends java.util.Vector<NucleotideSequence> {
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public ManyNucleotideSequences() {}
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public ManyNucleotideSequences(int initialCapacity) {
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this.setSize(initialCapacity);
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}
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public ManyNucleotideSequences(String seqpath) {
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ReferenceSequenceFile seqfile = ReferenceSequenceFileFactory.getReferenceSequenceFile(new File(seqpath));
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ReferenceSequence rs;
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while ((rs = seqfile.nextSequence()) != null) {
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byte[] bases = rs.getBases();
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NucleotideSequence ns = new NucleotideSequence(bases.length);
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for (int locus = 0; locus < bases.length; locus++) {
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Nucleotide nt;
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switch(bases[locus]) {
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case 'A': nt = Nucleotide.A; break;
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case 'C': nt = Nucleotide.C; break;
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case 'G': nt = Nucleotide.G; break;
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case 'T': nt = Nucleotide.T; break;
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default: nt = Nucleotide.T; break;
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}
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ns.set(locus, nt);
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}
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this.add(ns);
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}
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}
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public ManyNucleotideSequences reverseComplement() {
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for (int contig = 0; contig < this.size(); contig++) {
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this.get(contig).reverseComplement();
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}
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return this;
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}
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}
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package org.broadinstitute.sting.playground.fourbasecaller;
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import java.lang.String;
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public enum Nucleotide {
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A, C, G, T;
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Nucleotide complement() {
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switch (this) {
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case A: return T;
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case C: return G;
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case G: return C;
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case T: return A;
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}
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throw new IllegalArgumentException("Nucleotide must be A, C, G, or T.");
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}
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public char asChar() {
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switch(this) {
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case A: return 'A';
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case C: return 'C';
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case G: return 'G';
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case T: return 'T';
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}
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throw new IllegalArgumentException("Nucleotide must be A, C, G, or T.");
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}
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public String toString() {
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char[] value = new char[1];
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value[0] = this.asChar();
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return new String(value);
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}
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}
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package org.broadinstitute.sting.playground.fourbasecaller;
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import cern.colt.matrix.DoubleFactory2D;
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import cern.colt.matrix.DoubleMatrix2D;
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import cern.colt.matrix.linalg.Algebra;
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import org.broadinstitute.sting.playground.illumina.FourIntensity;
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public class NucleotideChannelCovariances {
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private DoubleMatrix2D[] covs;
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private int[] counts;
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public NucleotideChannelCovariances() {
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counts = new int[4];
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covs = new DoubleMatrix2D[4];
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for (int i = 0; i < 4; i++) {
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covs[i] = (DoubleFactory2D.dense).make(4, 4);
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}
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}
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public void add(Nucleotide nuc, FourIntensity sig, NucleotideChannelMeans mus) {
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FourIntensity f = new FourIntensity(sig);
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f.subtract(mus.channelMeans(nuc));
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DoubleMatrix2D cov = covs[nuc.ordinal()];
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for (int i = 0; i < 4; i++) {
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for (int j = 0; j < 4; j++) {
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cov.set(i, j, cov.get(i, j) + f.getChannelIntensity(i)*f.getChannelIntensity(j));
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}
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}
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counts[nuc.ordinal()]++;
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}
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public DoubleMatrix2D channelCovariances(Nucleotide base) {
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DoubleMatrix2D newcov = covs[base.ordinal()].copy();
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/*
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for (int i = 0; i < 4; i++) {
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for (int j = 0; j < 4; j++) {
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newcov.set(i, j, newcov.get(i, j)/((double) counts[base.ordinal()]));
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}
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}
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*/
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return newcov;
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}
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public void invert() {
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Algebra alg = new Algebra();
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for (int i = 0; i < 4; i++) {
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for (int j = 0; j < 4; j++) {
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for (int k = 0; k < 4; k++) {
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covs[i].set(j, k, covs[i].get(j, k)/((double) counts[i]));
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}
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}
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DoubleMatrix2D covinv = alg.inverse(covs[i]);
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covs[i] = covinv;
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}
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}
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}
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package org.broadinstitute.sting.playground.fourbasecaller;
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import org.broadinstitute.sting.playground.illumina.FourIntensity;
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public class NucleotideChannelMeans {
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private FourIntensity[] sigs;
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private int[] counts;
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public NucleotideChannelMeans() {
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counts = new int[4];
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sigs = new FourIntensity[4];
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for (int base = 0; base < 4; base++) {
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sigs[base] = new FourIntensity();
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}
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}
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public void add(Nucleotide base, FourIntensity intensity) {
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sigs[base.ordinal()].add(intensity);
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counts[base.ordinal()]++;
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}
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public FourIntensity channelMeans(Nucleotide base) {
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FourIntensity meansig = new FourIntensity(sigs[base.ordinal()]);
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meansig.divide(counts[base.ordinal()]);
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return meansig;
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}
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public float channelMean(Nucleotide base, int channel) {
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FourIntensity meansig = channelMeans(base);
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return meansig.getChannelIntensity(channel);
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}
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public String toString() {
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return "a:{" + channelMean(Nucleotide.A, 0) + " " + channelMean(Nucleotide.A, 1) + " " + channelMean(Nucleotide.A, 2) + " " + channelMean(Nucleotide.A, 3) + "} " +
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"c:{" + channelMean(Nucleotide.C, 0) + " " + channelMean(Nucleotide.C, 1) + " " + channelMean(Nucleotide.C, 2) + " " + channelMean(Nucleotide.C, 3) + "} " +
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"g:{" + channelMean(Nucleotide.G, 0) + " " + channelMean(Nucleotide.G, 1) + " " + channelMean(Nucleotide.G, 2) + " " + channelMean(Nucleotide.G, 3) + "} " +
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"t:{" + channelMean(Nucleotide.T, 0) + " " + channelMean(Nucleotide.T, 1) + " " + channelMean(Nucleotide.T, 2) + " " + channelMean(Nucleotide.T, 3) + "}";
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}
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}
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@ -1,59 +0,0 @@
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package org.broadinstitute.sting.playground.fourbasecaller;
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import org.broadinstitute.sting.playground.fourbasecaller.Nucleotide;
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import java.lang.String;
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import java.util.Vector;
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class NucleotideSequence extends java.util.Vector<Nucleotide> {
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public NucleotideSequence(int initialCapacity) {
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this.setSize(initialCapacity);
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}
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public NucleotideSequence(NucleotideSequence ns) {
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this.setSize(ns.size());
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for (int locus = 0; locus < ns.size(); locus++) {
|
||||
switch (ns.get(locus)) {
|
||||
case A: this.set(locus, Nucleotide.A); break;
|
||||
case C: this.set(locus, Nucleotide.C); break;
|
||||
case G: this.set(locus, Nucleotide.G); break;
|
||||
case T: this.set(locus, Nucleotide.T); break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public NucleotideSequence reverseComplement() {
|
||||
if (this.size() % 2 != 0) {
|
||||
this.get(this.size()/2 + 1).complement();
|
||||
}
|
||||
|
||||
for (int locus = 0; locus < this.size()/2; locus++) {
|
||||
Nucleotide temp = this.get(locus).complement();
|
||||
this.set(locus, this.get(this.size() - locus - 1).complement());
|
||||
this.set(this.size() - locus - 1, temp);
|
||||
}
|
||||
|
||||
return this;
|
||||
}
|
||||
|
||||
public int editDistance(NucleotideSequence ns) { return editDistance(ns, this.size() < ns.size() ? this.size() : ns.size()); }
|
||||
|
||||
public int editDistance(NucleotideSequence ns, int searchLength) {
|
||||
int editDistance = 0;
|
||||
for (int locus = 0; locus < searchLength; locus++) {
|
||||
editDistance += (this.get(locus) != ns.get(locus)) ? 1 : 0;
|
||||
}
|
||||
|
||||
return editDistance;
|
||||
}
|
||||
|
||||
public String toString() {
|
||||
char[] charbuffer = new char[this.size()];
|
||||
for (int locus = 0; locus < this.size(); locus++) {
|
||||
charbuffer[locus] = this.get(locus).asChar();
|
||||
}
|
||||
|
||||
return new String(charbuffer);
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue