made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1150 348d0f76-0448-11de-a6fe-93d51630548a
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aaron
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package org.broadinstitute.sting.utils.fasta;
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import org.broadinstitute.sting.utils.StingException;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.PrintStream;
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import java.util.List;
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/**
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* @author aaron
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* <p/>
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* Class ArtificialFastaUtils
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* <p/>
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* artificial fasta utility class, for generating fake fastas.
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*/
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public class ArtificialFastaUtils {
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public enum BASE_PATTERN {
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RANDOM, ALL_A, ALL_T, ALL_C, ALL_G;
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}
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// what bases we support
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public enum BASES {
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A, T, C, G;
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}
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// create an artificial fasta file
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public static void createArtificialFasta(String fileName,
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List<String> contigNames,
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List<Integer> contigSizes,
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BASE_PATTERN pattern) {
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PrintStream s;
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try {
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s = new PrintStream(new FileOutputStream(fileName));
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} catch (FileNotFoundException e) {
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throw new StingException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e);
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}
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generateFakeFasta(contigNames, contigSizes, pattern, s);
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}
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// create an artificial fasta file
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public static void createArtificialFasta(PrintStream stream,
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List<String> contigNames,
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List<Integer> contigSizes,
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BASE_PATTERN pattern) {
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generateFakeFasta(contigNames, contigSizes, pattern, stream);
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}
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/**
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* create a fake fasta file
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*
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* @param contigNames the pile of contig names
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* @param contigSizes the pile of contig sizes
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* @param pattern the pattern to use for the base distrobution
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* @param s the print stream to write to
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*/
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private static void generateFakeFasta(List<String> contigNames, List<Integer> contigSizes, BASE_PATTERN pattern, PrintStream s) {
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if (contigNames.size() != contigSizes.size()) {
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throw new StingException("ArtificialContig name and size arrays are not equal sizes");
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}
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for (int x = 0; x < contigNames.size(); x++) {
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ArtificialContig tig = new ArtificialContig(contigNames.get(x), contigSizes.get(x), pattern);
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tig.write(s);
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}
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s.close();
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}
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}
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/** the fake contig class, a fasta is made up of these */
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class ArtificialContig {
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public static final int COLUMN_WIDTH = 80;
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final protected String mName;
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final protected int mSize;
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final protected ArtificialFastaUtils.BASE_PATTERN mPattern;
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public ArtificialContig(String name, int size, ArtificialFastaUtils.BASE_PATTERN pat) {
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this.mName = name;
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this.mSize = size;
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this.mPattern = pat;
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}
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/**
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* write out the contig to a stream
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*
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* @param stream
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*/
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public void write(PrintStream stream) {
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stream.println(">" + mName);
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int count = 0;
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while (count < mSize) {
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for (int x = 0; x < COLUMN_WIDTH; x++) {
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stream.print(generateAppropriateBase());
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count++;
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if (count >= mSize) {
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break;
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}
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}
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stream.println();
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}
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}
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/**
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* generate the appropriate base, given the BASE_PATTERN
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*
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* @return a base, as a string
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*/
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public String generateAppropriateBase() {
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switch (mPattern) {
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case RANDOM:
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return (ArtificialFastaUtils.BASES.values()[(int) Math.round(Math.random() * 4)]).toString();
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case ALL_A:
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return "A";
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case ALL_T:
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return "T";
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case ALL_C:
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return "C";
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case ALL_G:
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return "G";
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default:
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throw new StingException("Unknown base pattern");
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}
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}
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}
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@ -0,0 +1,28 @@
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package org.broadinstitute.sting.utils.sam;
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/**
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*
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* @author aaron
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*
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* Class ArtificialSAMGenerator
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*
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* This provides for an external utility, that creates sam files and associates fasta files
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*/
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public class ArtificialSAMGenerator {
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}
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class ArtificialFASTAUtils {
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}
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@ -161,7 +161,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator implements
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contigIndex = rec.getSequenceIndex();
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}
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}
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if (contigIndex < 0) { throw new IllegalArgumentException("Contig" + contig + " doesn't exist"); }
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if (contigIndex < 0) { throw new IllegalArgumentException("ArtificialContig" + contig + " doesn't exist"); }
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while (super.hasNext() && this.peek().getReferenceIndex() < contigIndex) {
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super.next();
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}
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@ -1,30 +1,12 @@
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package org.broadinstitute.sting.utils.sam;
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import net.sf.samtools.*;
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import java.io.File;
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import java.util.*;
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import org.broadinstitute.sting.gatk.iterators.QueryIterator;
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import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
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import org.broadinstitute.sting.utils.StingException;
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/**
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*
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* User: aaron
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* Date: May 21, 2009
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* Time: 2:57:48 PM
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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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*/
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import java.io.File;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* @author aaron
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@ -46,11 +28,11 @@ public class ArtificialSAMUtils {
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SAMFileHeader header = createArtificialSamHeader(numberOfChromosomes, startingChromosome, chromosomeSize);
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File outFile = new File(filename);
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SAMFileWriter out = new SAMFileWriterFactory().makeBAMWriter(header, false, outFile);
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SAMFileWriter out = new SAMFileWriterFactory().makeBAMWriter(header, true, outFile);
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for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) {
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for (int readNumber = 0; readNumber < readsPerChomosome; readNumber++) {
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out.addAlignment(createArtificialRead(header, "Read_" + readNumber, x - startingChromosome, readNumber, 100));
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for (int readNumber = 1; readNumber < readsPerChomosome; readNumber++) {
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out.addAlignment(createArtificialRead(header, "Read_" + readNumber, x - startingChromosome, readNumber, DEFAULT_READ_LENGTH));
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}
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}
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@ -73,7 +55,7 @@ public class ArtificialSAMUtils {
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SAMFileWriter out = new SAMFileWriterFactory().makeSAMWriter(header, false, outFile);
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for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) {
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for (int readNumber = 0; readNumber < readsPerChomosome; readNumber++) {
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for (int readNumber = 1; readNumber <= readsPerChomosome; readNumber++) {
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out.addAlignment(createArtificialRead(header, "Read_" + readNumber, x - startingChromosome, readNumber, 100));
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}
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}
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@ -92,6 +74,7 @@ public class ArtificialSAMUtils {
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*/
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public static SAMFileHeader createArtificialSamHeader( int numberOfChromosomes, int startingChromosome, int chromosomeSize ) {
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SAMFileHeader header = new SAMFileHeader();
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header.setSortOrder(net.sf.samtools.SAMFileHeader.SortOrder.coordinate);
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SAMSequenceDictionary dict = new SAMSequenceDictionary();
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// make up some sequence records
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for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) {
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*/
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public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, int length ) {
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if (alignmentStart == 0)
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throw new StingException("Invalid alignment start for artificial read");
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throw new StingException("Invalid alignment start for artificial read, start = " + alignmentStart);
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SAMRecord record = new SAMRecord(header);
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record.setReadName(name);
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record.setReferenceIndex(refIndex);
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@ -0,0 +1,43 @@
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package org.broadinstitute.sting.utils.fasta;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
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import org.junit.Assert;
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import org.junit.Test;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* @author aaron
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* <p/>
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* Class ArtificialFastaUtilsTest
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* <p/>
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* test out the ArtificialFastaUtils functionality
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*/
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public class ArtificialFastaUtilsTest extends BaseTest {
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/** generate a fake fasta */
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@Test
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public void testFastaGeneration() {
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List<String> names = new ArrayList<String>();
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List<Integer> sizes = new ArrayList<Integer>();
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for (int x = 0; x < 5; x++) {
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sizes.add(1000);
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names.add("chr" + (x+1));
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}
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File temp = new File("tempFileFasta.fasta");
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ArtificialFastaUtils.createArtificialFasta(temp.getName(),names,sizes,ArtificialFastaUtils.BASE_PATTERN.ALL_A);
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// using the fasta sequence file to test, in reality we should use the indexed version
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FastaSequenceFile2 fasta = new FastaSequenceFile2(temp);
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Assert.assertEquals(5,fasta.getSequenceDictionary().getSequences().size());
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ArtificialSAMUtils.createArtificialBamFile("tempFileBAM.bam",5,1,1000,600);
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//temp.delete();
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}
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}
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