Class to read an .fai file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@405 348d0f76-0448-11de-a6fe-93d51630548a
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package org.broadinstitute.sting.utils;
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import edu.mit.broad.picard.PicardException;
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import java.util.Scanner;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.regex.MatchResult;
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import java.util.regex.Pattern;
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import java.util.regex.Matcher;
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import java.io.File;
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import java.io.FileNotFoundException;
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/**
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* Created by IntelliJ IDEA.
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* User: hanna
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* Date: Apr 14, 2009
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* Time: 10:02:10 AM
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*
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* Reads a fasta index file (.fai).
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*/
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public class FastaSequenceIndex {
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private Map<String,FastaSequenceIndexEntry> sequenceEntries =
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new HashMap<String,FastaSequenceIndexEntry>();
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/**
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* Build a sequence index from the specified file.
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* @param indexFile File to open.
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* @throws PicardException if file is of invalid format.
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*/
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public FastaSequenceIndex( File indexFile ) throws FileNotFoundException {
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Scanner scanner = new Scanner(indexFile);
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while( scanner.hasNext() ) {
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// Tokenize and validate the index line.
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String result = scanner.findInLine("(\\w+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
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if( result == null )
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throw new PicardException("Found invalid line in index file:" + scanner.nextLine());
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MatchResult tokens = scanner.match();
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if( tokens.groupCount() != 5 )
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throw new PicardException("Found invalid line in index file:" + scanner.nextLine());
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// Skip past the line separator
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scanner.nextLine();
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// Parse the index line.
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String contig = tokens.group(1);
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long size = Long.valueOf(tokens.group(2));
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long location = Long.valueOf(tokens.group(3));
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int basesPerLine = Integer.valueOf(tokens.group(4));
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int bytesPerLine = Integer.valueOf(tokens.group(5));
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// Build sequence structure
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sequenceEntries.put( contig,new FastaSequenceIndexEntry(contig,location,size,basesPerLine,bytesPerLine) );
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}
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}
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/**
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* Does the given contig name have a corresponding entry?
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* @param contigName The contig name for which to search.
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* @return True if contig name is present; false otherwise.
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*/
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public boolean hasIndexEntry( String contigName ) {
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return sequenceEntries.containsKey(contigName);
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}
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/**
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* Retrieve the index entry associated with the given contig.
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* @param contigName Name of the contig for which to search.
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* @return Index entry associated with the given contig.
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* @throws PicardException if the associated index entry can't be found.
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*/
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public FastaSequenceIndexEntry getIndexEntry( String contigName ) {
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if( !hasIndexEntry(contigName) )
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throw new PicardException("Unable to find entry for contig: " + contigName);
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return sequenceEntries.get(contigName);
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}
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}
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class FastaSequenceIndexEntry {
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private String contig;
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private long location;
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private long size;
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private int basesPerLine;
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private int bytesPerLine;
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public FastaSequenceIndexEntry( String contig,
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long location,
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long size,
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int basesPerLine,
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int bytesPerLine ) {
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this.contig = contig;
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this.location = location;
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this.size = size;
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this.basesPerLine = basesPerLine;
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this.bytesPerLine = bytesPerLine;
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}
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/**
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* Gets the contig associated with this entry.
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* @return String representation of the contig.
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*/
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public String getContig() {
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return contig;
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}
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/**
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* Gets the location of this contig within the fasta.
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* @return seek position within the fasta.
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*/
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public long getLocation() {
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return location;
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}
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/**
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* Gets the size, in bytes, of the data in the contig.
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* @return size of the contig bases in bytes.
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*/
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public long getSize() {
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return size;
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}
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/**
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* Gets the number of bases in a given line.
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* @return Number of bases in the fasta line.
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*/
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public int getBasesPerLine() {
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return basesPerLine;
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}
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/**
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* How many bytes (bases + whitespace) are consumed by the
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* given line?
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* @return Number of bytes in a line.
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*/
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public int getBytesPerLine() {
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return bytesPerLine;
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}
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public String toString() {
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return String.format("contig %s; location %d; size %d; basesPerLine %d; bytesPerLine %d", contig,
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location,
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size,
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basesPerLine,
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bytesPerLine );
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}
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}
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@ -0,0 +1,127 @@
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package org.broadinstitute.sting.utils;
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import org.junit.BeforeClass;
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import org.junit.Before;
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import org.junit.Test;
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import org.junit.Assert;
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import org.apache.log4j.BasicConfigurator;
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import java.io.File;
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import java.io.FileNotFoundException;
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import edu.mit.broad.picard.PicardException;
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/**
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* Created by IntelliJ IDEA.
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* User: hanna
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* Date: Apr 14, 2009
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* Time: 10:34:15 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class FastaSequenceIndexTest {
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private final String sequenceIndexName = "/Volumes/ifs/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai";
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private FastaSequenceIndex sequenceIndex = null;
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@BeforeClass
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public static void initialize() {
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BasicConfigurator.configure();
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}
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@Before
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public void doForEachTest() throws FileNotFoundException {
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sequenceIndex = new FastaSequenceIndex( new File(sequenceIndexName) );
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}
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@Test
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public void testInitialContig() {
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Assert.assertTrue("Contig chrM is not present", sequenceIndex.hasIndexEntry("chrM"));
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FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chrM");
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Assert.assertEquals("Contig chrM name is incorrect",entry.getContig(),"chrM");
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Assert.assertEquals("Contig chrM location is incorrect",entry.getLocation(),6L);
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Assert.assertEquals("Contig chrM size is incorrect",entry.getSize(),16571L);
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Assert.assertEquals("Contig chrM bases per line is incorrect",entry.getBasesPerLine(),50);
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Assert.assertEquals("Contig chrM bytes per line is incorrect",entry.getBytesPerLine(),51);
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}
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@Test
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public void testMiddleContig() {
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Assert.assertTrue("Contig chr8 is not present", sequenceIndex.hasIndexEntry("chr8"));
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FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chr8");
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Assert.assertEquals("Contig chr8 name is incorrect",entry.getContig(),"chr8");
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Assert.assertEquals("Contig chr8 location is incorrect",entry.getLocation(),1419403101L);
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Assert.assertEquals("Contig chr8 size is incorrect",entry.getSize(),146274826L);
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Assert.assertEquals("Contig chr8 bases per line is incorrect",entry.getBasesPerLine(),50);
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Assert.assertEquals("Contig chr8 bytes per line is incorrect",entry.getBytesPerLine(),51);
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}
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@Test
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public void testLastContig() {
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Assert.assertTrue("Contig chrX_random is not present", sequenceIndex.hasIndexEntry("chrX_random"));
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FastaSequenceIndexEntry entry = sequenceIndex.getIndexEntry("chrX_random");
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Assert.assertEquals("Contig chrX_random name is incorrect",entry.getContig(),"chrX_random");
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Assert.assertEquals("Contig chrX_random location is incorrect",entry.getLocation(),3156698441L);
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Assert.assertEquals("Contig chrX_random size is incorrect",entry.getSize(),1719168L);
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Assert.assertEquals("Contig chrX_random bases per line is incorrect",entry.getBasesPerLine(),50);
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Assert.assertEquals("Contig chrX_random bytes per line is incorrect",entry.getBytesPerLine(),51);
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}
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@Test
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public void testAllContigsPresent() {
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Assert.assertTrue("Contig chrM is not present", sequenceIndex.hasIndexEntry("chrM"));
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Assert.assertTrue("Contig chr1 is not present", sequenceIndex.hasIndexEntry("chr1"));
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Assert.assertTrue("Contig chr2 is not present", sequenceIndex.hasIndexEntry("chr2"));
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Assert.assertTrue("Contig chr3 is not present", sequenceIndex.hasIndexEntry("chr3"));
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Assert.assertTrue("Contig chr4 is not present", sequenceIndex.hasIndexEntry("chr4"));
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Assert.assertTrue("Contig chr5 is not present", sequenceIndex.hasIndexEntry("chr5"));
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Assert.assertTrue("Contig chr6 is not present", sequenceIndex.hasIndexEntry("chr6"));
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Assert.assertTrue("Contig chr7 is not present", sequenceIndex.hasIndexEntry("chr7"));
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Assert.assertTrue("Contig chr8 is not present", sequenceIndex.hasIndexEntry("chr8"));
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Assert.assertTrue("Contig chr9 is not present", sequenceIndex.hasIndexEntry("chr9"));
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Assert.assertTrue("Contig chr10 is not present", sequenceIndex.hasIndexEntry("chr10"));
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Assert.assertTrue("Contig chr11 is not present", sequenceIndex.hasIndexEntry("chr11"));
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Assert.assertTrue("Contig chr12 is not present", sequenceIndex.hasIndexEntry("chr12"));
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Assert.assertTrue("Contig chr13 is not present", sequenceIndex.hasIndexEntry("chr13"));
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Assert.assertTrue("Contig chr14 is not present", sequenceIndex.hasIndexEntry("chr14"));
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Assert.assertTrue("Contig chr15 is not present", sequenceIndex.hasIndexEntry("chr15"));
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Assert.assertTrue("Contig chr16 is not present", sequenceIndex.hasIndexEntry("chr16"));
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Assert.assertTrue("Contig chr17 is not present", sequenceIndex.hasIndexEntry("chr17"));
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Assert.assertTrue("Contig chr18 is not present", sequenceIndex.hasIndexEntry("chr18"));
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Assert.assertTrue("Contig chr19 is not present", sequenceIndex.hasIndexEntry("chr19"));
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Assert.assertTrue("Contig chr20 is not present", sequenceIndex.hasIndexEntry("chr20"));
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Assert.assertTrue("Contig chr21 is not present", sequenceIndex.hasIndexEntry("chr21"));
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Assert.assertTrue("Contig chr22 is not present", sequenceIndex.hasIndexEntry("chr22"));
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Assert.assertTrue("Contig chrX is not present", sequenceIndex.hasIndexEntry("chrX"));
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Assert.assertTrue("Contig chrY is not present", sequenceIndex.hasIndexEntry("chrY"));
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Assert.assertTrue("Contig chr1_random is not present", sequenceIndex.hasIndexEntry("chr1_random"));
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Assert.assertTrue("Contig chr2_random is not present", sequenceIndex.hasIndexEntry("chr2_random"));
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Assert.assertTrue("Contig chr3_random is not present", sequenceIndex.hasIndexEntry("chr3_random"));
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Assert.assertTrue("Contig chr4_random is not present", sequenceIndex.hasIndexEntry("chr4_random"));
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Assert.assertTrue("Contig chr5_random is not present", sequenceIndex.hasIndexEntry("chr5_random"));
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Assert.assertTrue("Contig chr6_random is not present", sequenceIndex.hasIndexEntry("chr6_random"));
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Assert.assertTrue("Contig chr7_random is not present", sequenceIndex.hasIndexEntry("chr7_random"));
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Assert.assertTrue("Contig chr8_random is not present", sequenceIndex.hasIndexEntry("chr8_random"));
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Assert.assertTrue("Contig chr9_random is not present", sequenceIndex.hasIndexEntry("chr9_random"));
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Assert.assertTrue("Contig chr10_random is not present", sequenceIndex.hasIndexEntry("chr10_random"));
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Assert.assertTrue("Contig chr11_random is not present", sequenceIndex.hasIndexEntry("chr11_random"));
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Assert.assertTrue("Contig chr13_random is not present", sequenceIndex.hasIndexEntry("chr13_random"));
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Assert.assertTrue("Contig chr15_random is not present", sequenceIndex.hasIndexEntry("chr15_random"));
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Assert.assertTrue("Contig chr16_random is not present", sequenceIndex.hasIndexEntry("chr16_random"));
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Assert.assertTrue("Contig chr17_random is not present", sequenceIndex.hasIndexEntry("chr17_random"));
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Assert.assertTrue("Contig chr18_random is not present", sequenceIndex.hasIndexEntry("chr18_random"));
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Assert.assertTrue("Contig chr19_random is not present", sequenceIndex.hasIndexEntry("chr19_random"));
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Assert.assertTrue("Contig chr21_random is not present", sequenceIndex.hasIndexEntry("chr21_random"));
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Assert.assertTrue("Contig chr22_random is not present", sequenceIndex.hasIndexEntry("chr22_random"));
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Assert.assertTrue("Contig chrX_random is not present", sequenceIndex.hasIndexEntry("chrX_random"));
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}
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@Test
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public void testHasInvalidEntry() {
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Assert.assertFalse("Found an invalid entry", sequenceIndex.hasIndexEntry("invalid"));
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}
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@Test(expected= PicardException.class)
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public void testGetInvalidEntry() {
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sequenceIndex.getIndexEntry("invalid");
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}
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}
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