485 lines
18 KiB
Java
485 lines
18 KiB
Java
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package org.broadinstitute.sting.utils;
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import edu.mit.broad.picard.directed.IntervalList;
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import edu.mit.broad.picard.util.Interval;
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import net.sf.picard.reference.ReferenceSequenceFile;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMSequenceDictionary;
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import net.sf.samtools.SAMSequenceRecord;
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import org.apache.log4j.Logger;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Iterator;
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import java.util.List;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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/**
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* Created by IntelliJ IDEA.
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* User: aaronmckenna
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* Date: Jun 18, 2009
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* Time: 11:17:01 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class GenomeLocParser {
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private static Logger logger = Logger.getLogger(GenomeLocParser.class);
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// --------------------------------------------------------------------------------------------------------------
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//
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// Ugly global variable defining the optional ordering of contig elements
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//
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// --------------------------------------------------------------------------------------------------------------
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//public static Map<String, Integer> refContigOrdering = null;
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private static SAMSequenceDictionary contigInfo = null;
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/**
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* do we have a contig ordering setup?
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*
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* @return true if the contig order is setup
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*/
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public static boolean hasKnownContigOrdering() {
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return contigInfo != null;
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}
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/**
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* get the contig's SAMSequenceRecord
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*
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* @param contig the string name of the contig
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*
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* @return the sam sequence record
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*/
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public static SAMSequenceRecord getContigInfo(final String contig) {
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return contigInfo.getSequence(contig);
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}
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/**
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* Returns the contig index of a specified string version of the contig
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*
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* @param contig the contig string
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*
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* @return the contig index, -1 if not found
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*/
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public static int getContigIndex(final String contig) {
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if (contigInfo.getSequenceIndex(contig) == -1)
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Utils.scareUser(String.format("Contig %s given as location, but this contig isn't present in the Fasta sequence dictionary", contig));
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return contigInfo.getSequenceIndex(contig);
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}
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/**
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* set our internal reference contig order
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*
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* @param refFile the reference file
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*
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* @return true if we were successful
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*/
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public static boolean setupRefContigOrdering(final ReferenceSequenceFile refFile) {
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return setupRefContigOrdering(refFile.getSequenceDictionary());
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}
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/**
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* setup our internal reference contig order
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*
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* @param seqDict the sequence dictionary
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*
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* @return true if we were successful
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*/
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public static boolean setupRefContigOrdering(final SAMSequenceDictionary seqDict) {
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if (seqDict == null) { // we couldn't load the reference dictionary
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logger.info("Failed to load reference dictionary, falling back to lexicographic order for contigs");
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Utils.scareUser("Failed to load reference dictionary");
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return false;
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} else if (contigInfo == null) {
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contigInfo = seqDict;
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logger.debug(String.format("Prepared reference sequence contig dictionary"));
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for (SAMSequenceRecord contig : seqDict.getSequences()) {
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logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength()));
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}
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}
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GenomeLoc.MAX_CONTIG = contigInfo.getSequences().size();
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return true;
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}
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/**
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* parse a genome location, from a location string
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*
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* @param str the string to parse
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*
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* @return a GenomeLoc representing the String
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*/
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public static GenomeLoc parseGenomeLoc(final String str) {
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// 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
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//System.out.printf("Parsing location '%s'%n", str);
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final Pattern regex1 = Pattern.compile("([\\w&&[^:]]+)$"); // matches case 1
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final Pattern regex2 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)$"); // matches case 2
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final Pattern regex3 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)-([\\d,]+)$"); // matches case 3
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final Pattern regex4 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)\\+"); // matches case 4
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String contig = null;
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long start = 1;
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long stop = Integer.MAX_VALUE;
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boolean bad = false;
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Matcher match1 = regex1.matcher(str);
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Matcher match2 = regex2.matcher(str);
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Matcher match3 = regex3.matcher(str);
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Matcher match4 = regex4.matcher(str);
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try {
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if (match1.matches()) {
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contig = match1.group(1);
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} else if (match2.matches()) {
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contig = match2.group(1);
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start = parsePosition(match2.group(2));
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stop = start;
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} else if (match4.matches()) {
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contig = match4.group(1);
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start = parsePosition(match4.group(2));
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} else if (match3.matches()) {
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contig = match3.group(1);
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start = parsePosition(match3.group(2));
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stop = parsePosition(match3.group(3));
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if (start > stop)
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bad = true;
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} else {
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bad = true;
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}
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} catch (Exception e) {
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bad = true;
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}
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if (bad) {
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throw new StingException("Invalid Genome Location string: " + str);
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}
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if (stop == Integer.MAX_VALUE && hasKnownContigOrdering()) {
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// lookup the actually stop position!
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stop = getContigInfo(contig).getSequenceLength();
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}
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if (!isContigValid(contig))
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throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
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GenomeLoc loc = parseGenomeLoc(contig, start, stop);
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// System.out.printf(" => Parsed location '%s' into %s%n", str, loc);
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return loc;
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}
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/**
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* Useful utility function that parses a location string into a coordinate-order sorted
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* array of GenomeLoc objects
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*
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* @param str String representation of genome locs. Null string corresponds to no filter.
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*
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* @return Array of GenomeLoc objects corresponding to the locations in the string, sorted by coordinate order
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*/
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public static List<GenomeLoc> parseGenomeLocs(final String str) {
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// Null string means no filter.
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if (str == null) return null;
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// Of the form: loc1;loc2;...
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// Where each locN can be:
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// 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
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try {
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List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
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for (String loc : str.split(";"))
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locs.add(parseGenomeLoc(loc.trim()));
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Collections.sort(locs);
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//logger.info(String.format("Going to process %d locations", locs.length));
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locs = mergeOverlappingLocations(locs);
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logger.debug("Locations are:" + Utils.join(", ", locs));
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return locs;
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} catch (Exception e) { // TODO: fix this so that it passes the message from the exception, and doesn't print it out
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throw new StingException(String.format("Invalid locations string: %s, format is loc1;loc2; where each locN can be 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'", str),e);
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}
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}
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// --------------------------------------------------------------------------------------------------------------
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//
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// Parsing string representations
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//
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// --------------------------------------------------------------------------------------------------------------
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private static long parsePosition(final String pos) {
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String x = pos.replaceAll(",", "");
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return Long.parseLong(x);
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}
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/**
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* merge a list of genome locs that may be overlapping, returning the list of unique genomic locations
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*
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* @param raw the unchecked genome loc list
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*
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* @return the list of merged locations
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*/
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public static List<GenomeLoc> mergeOverlappingLocations(final List<GenomeLoc> raw) {
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logger.debug(" Raw locations are:\n" + Utils.join("\n", raw));
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if (raw.size() <= 1)
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return raw;
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else {
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ArrayList<GenomeLoc> merged = new ArrayList<GenomeLoc>();
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Iterator<GenomeLoc> it = raw.iterator();
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GenomeLoc prev = it.next();
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while (it.hasNext()) {
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GenomeLoc curr = it.next();
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if (prev.contiguousP(curr)) {
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prev = prev.merge(curr);
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} else {
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merged.add(prev);
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prev = curr;
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}
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}
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merged.add(prev);
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return merged;
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}
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}
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/**
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* Determines whether the given contig is valid with respect to the sequence dictionary
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* already installed in the GenomeLoc.
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*
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* @return True if the contig is valid. False otherwise.
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*/
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private static boolean isContigValid(String contig) {
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int contigIndex = contigInfo.getSequenceIndex(contig);
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return isSequenceIndexValid(contigIndex);
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}
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/**
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* Determines whether the given sequence index is valid with respect to the sequence dictionary.
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*
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* @param sequenceIndex sequence index
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*
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* @return True if the sequence index is valid, false otherwise.
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*/
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private static boolean isSequenceIndexValid(int sequenceIndex) {
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return sequenceIndex >= 0 && sequenceIndex < contigInfo.size();
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}
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/**
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* Use this static constructor when the input data is under limited control (i.e. parsing user data).
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*
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* @param contig Contig to parse.
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* @param start Starting point.
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* @param stop Stop point.
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*
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* @return The genome location, or a MalformedGenomeLocException if unparseable.
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*/
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public static GenomeLoc parseGenomeLoc(final String contig, long start, long stop) {
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if (!isContigValid(contig))
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throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
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return new GenomeLoc(contig, getContigIndex(contig), start, stop);
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}
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/**
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* Read a file of genome locations to process.
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* regions specified by the location string. The string is of the form:
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* Of the form: loc1;loc2;...
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* Where each locN can be:
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* 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
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*
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* @param file_name
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*/
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public static List<GenomeLoc> intervalFileToList(final String file_name) {
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/**
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* first try to read it as an interval file since that's well structured
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* we'll fail quickly if it's not a valid file. Then try to parse it as
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* a location string file
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*/
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List<GenomeLoc> ret = null;
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try {
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IntervalList il = IntervalList.fromFile(new File(file_name));
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// iterate through the list of merged intervals and add then as GenomeLocs
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ret = new ArrayList<GenomeLoc>();
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for (Interval interval : il.getUniqueIntervals()) {
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ret.add(new GenomeLoc(interval.getSequence(), getContigIndex(interval.getSequence()), interval.getStart(), interval.getEnd()));
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}
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return ret;
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} catch (Exception e) {
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try {
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xReadLines reader = new xReadLines(new File(file_name));
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List<String> lines = reader.readLines();
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reader.close();
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String locStr = Utils.join(";", lines);
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logger.debug("locStr: " + locStr);
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ret = parseGenomeLocs(locStr);
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return ret;
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} catch (Exception e2) {
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logger.error("Attempt to parse interval file in GATK format failed: " + e2.getMessage());
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e2.printStackTrace();
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throw new StingException("Unable to parse out interval file in either format", e);
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}
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}
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}
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/**
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* get the sequence name from a sequence index
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*
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* @param contigIndex get the contig index
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*
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* @return the string that represents that contig name
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*/
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private static String getSequenceNameFromIndex(int contigIndex) {
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return GenomeLocParser.contigInfo.getSequence(contigIndex).getSequenceName();
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}
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/**
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* create a genome loc, given the contig name, start, and stop
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*
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* @param contig the contig name
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* @param start the starting position
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* @param stop the stop position
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*
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* @return a new genome loc
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*/
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public static GenomeLoc createGenomeLoc(String contig, final long start, final long stop) {
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checkSetup();
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return verifyGenomeLoc(new GenomeLoc(contig, GenomeLocParser.getContigIndex(contig), start, stop));
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}
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/**
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* create a genome loc, given the contig index, start, and stop
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*
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* @param contigIndex the contig index
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* @param start the start position
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* @param stop the stop position
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*
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* @return a new genome loc
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*/
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public static GenomeLoc createGenomeLoc(int contigIndex, final long start, final long stop) {
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checkSetup();
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if (start < 0) {
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throw new StingException("Bad start position " + start);
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}
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if (stop < -1) {
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throw new StingException("Bad stop position " + stop);
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} // a negative -1 indicates it's not a meaningful end position
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return new GenomeLoc(getSequenceNameFromIndex(contigIndex), contigIndex, start, stop);
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}
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/**
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* create a genome loc, given a read
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*
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* @param read
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*
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* @return
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*/
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public static GenomeLoc createGenomeLoc(final SAMRecord read) {
|
||
|
|
checkSetup();
|
||
|
|
return verifyGenomeLoc(new GenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getAlignmentStart(), read.getAlignmentEnd()));
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
/**
|
||
|
|
* create a new genome loc, given the contig position, and a single position
|
||
|
|
*
|
||
|
|
* @param contig the contig name
|
||
|
|
* @param pos the postion
|
||
|
|
*
|
||
|
|
* @return a genome loc representing a single base at the specified postion on the contig
|
||
|
|
*/
|
||
|
|
public static GenomeLoc createGenomeLoc(final int contig, final long pos) {
|
||
|
|
checkSetup();
|
||
|
|
return verifyGenomeLoc(new GenomeLoc(getSequenceNameFromIndex(contig), contig, pos, pos));
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* create a new genome loc, given the contig name, and a single position
|
||
|
|
*
|
||
|
|
* @param contig the contig name
|
||
|
|
* @param pos the postion
|
||
|
|
*
|
||
|
|
* @return a genome loc representing a single base at the specified postion on the contig
|
||
|
|
*/
|
||
|
|
public static GenomeLoc createGenomeLoc(final String contig, final long pos) {
|
||
|
|
checkSetup();
|
||
|
|
return verifyGenomeLoc(new GenomeLoc(contig, GenomeLocParser.getContigIndex(contig), pos, pos));
|
||
|
|
}
|
||
|
|
|
||
|
|
public static GenomeLoc createGenomeLoc(final GenomeLoc toCopy) {
|
||
|
|
checkSetup();
|
||
|
|
return verifyGenomeLoc(new GenomeLoc(toCopy.getContig(), toCopy.getContigIndex(), toCopy.getStart(), toCopy.getStop()));
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* verify the specified genome loc is valid, if it's not, throw an exception
|
||
|
|
*
|
||
|
|
* @param toReturn teh genome loc we're about to return
|
||
|
|
*
|
||
|
|
* @return the genome loc if it's valid, otherwise we throw an exception
|
||
|
|
*/
|
||
|
|
private static GenomeLoc verifyGenomeLoc(GenomeLoc toReturn) {
|
||
|
|
// conditions to fail on - we currently use a start of zero to indicate infinite read count, so don't check for that
|
||
|
|
//if ((toReturn.getStop() < toReturn.getStart())) {
|
||
|
|
// throw new StingException("Parameters to GenomeLocParser are incorrect: the start position is after the stop (Start = " + toReturn.getStart() + " stop = " + toReturn.getStop() + ")");
|
||
|
|
//}
|
||
|
|
if (toReturn.getStart() < 0) {
|
||
|
|
throw new StingException("Parameters to GenomeLocParser are incorrect: the start position is less than 0");
|
||
|
|
}
|
||
|
|
if (toReturn.getStop() < 0) {
|
||
|
|
throw new StingException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0");
|
||
|
|
}
|
||
|
|
if (toReturn.getContigIndex() < 0) {
|
||
|
|
throw new StingException("Parameters to GenomeLocParser are incorrect: the contig index is less than 0");
|
||
|
|
}
|
||
|
|
if (toReturn.getContigIndex() >= contigInfo.getSequences().size()) {
|
||
|
|
throw new StingException("Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count");
|
||
|
|
|
||
|
|
}
|
||
|
|
return toReturn;
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Move this Genome loc to the next contig, with a start
|
||
|
|
* and stop of 1.
|
||
|
|
*
|
||
|
|
* @return true if we are not out of contigs, otherwise false if we're
|
||
|
|
* at the end of the genome (no more contigs to jump to).
|
||
|
|
*/
|
||
|
|
public static GenomeLoc toNextContig(GenomeLoc current) {
|
||
|
|
if (current.getContigIndex() + 1 >= contigInfo.getSequences().size()) {
|
||
|
|
return null;
|
||
|
|
} else
|
||
|
|
return verifyGenomeLoc(new GenomeLoc(getSequenceNameFromIndex(current.getContigIndex() + 1), current.getContigIndex() + 1, 1, 1));
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* check to make sure that we've setup the contig information
|
||
|
|
*/
|
||
|
|
private static void checkSetup() {
|
||
|
|
if (contigInfo == null) {
|
||
|
|
throw new StingException("The GenomeLocParser hasn't been setup with a contig sequence yet");
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* compare two contig names, in the current context
|
||
|
|
*
|
||
|
|
* @param firstContig
|
||
|
|
* @param secondContig
|
||
|
|
*
|
||
|
|
* @return
|
||
|
|
*/
|
||
|
|
public static int compareContigs(String firstContig, String secondContig) {
|
||
|
|
checkSetup();
|
||
|
|
Integer ref1 = GenomeLocParser.getContigIndex(firstContig);
|
||
|
|
Integer ref2 = GenomeLocParser.getContigIndex(secondContig);
|
||
|
|
return ref1.compareTo(ref2);
|
||
|
|
|
||
|
|
}
|
||
|
|
}
|