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/*
* Copyright (C) 2009-2010 Institute for Computational Biomedicine,
* Weill Medical College of Cornell University
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.campagnelab.goby.modes;
import com.google.protobuf.ByteString;
import com.martiansoftware.jsap.JSAPException;
import com.martiansoftware.jsap.JSAPResult;
import it.unimi.dsi.fastutil.bytes.ByteArrayList;
import org.campagnelab.goby.alignments.*;
import org.campagnelab.goby.alignments.filters.AlignmentQualityFilter;
import org.campagnelab.goby.reads.ReadSet;
import org.campagnelab.goby.reads.Reads;
import org.campagnelab.goby.reads.ReadsReader;
import org.campagnelab.goby.util.WarningCounter;
import edu.cornell.med.icb.identifier.IndexedIdentifier;
import it.unimi.dsi.fastutil.objects.ObjectArrayList;
import it.unimi.dsi.lang.MutableString;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
/**
* Abstract class for modes that convert alignment formats to compact format.
* The JSAP file of the concrete implementation must include the following options in addition to the options specific
* to the concrete mode.
* <p/>
* "input"
* "output"
* "query-reads-ids"
* "target-reference-ids"
* "propagate-query-ids"
* "propagate-target-ids"
* "read-index-filter"
* "ambiguity-threshold"
* "quality-filter-parameters"
* <p/>
* <p/>
*
* @author Stuart Andrews
* Date: Sep 11, 2009
* Time: 9:30:16 PM
*/
public abstract class AbstractAlignmentToCompactMode extends AbstractGobyMode {
/**
* Used to log debug and informational messages.
*/
private static final Log LOG = LogFactory.getLog(AbstractAlignmentToCompactMode.class);
/**
* default ambiguity threshold.
*/
protected static final int DEFAULT_M_PARAM = 1;
/**
* Input file.
*/
protected String inputFile;
/**
* Output file.
*/
protected String outputFile;
/**
* Query / target identifiers.
*/
protected String queryReadIdsFilename;
protected String targetReferenceIdsFilename;
protected boolean propagateQueryIds;
protected boolean propagateTargetIds;
/**
* Conversion parameters.
*/
protected String qualityFilterParameters = "";
protected AlignmentQualityFilter qualityFilter;
protected File readIndexFilterFile;
protected int mParameter = DEFAULT_M_PARAM;
protected int numberOfReads = -1;
/**
* Identifiers for the query sequences in this alignment.
*/
protected final IndexedIdentifier queryIds = new IndexedIdentifier();
/**
* Identifiers for the target sequences in this alignment.
*/
protected final IndexedIdentifier targetIds = new IndexedIdentifier();
protected int numberOfReadsFromCommandLine;
/**
* Indicate that the file being imported is from a third party. This means that:
* <ol>
* <li>queryNames are not integers, but are strings that need to be converted to indices.</li>
* <li>targetNames should be treated as strings and defined from the input.</li>
* <li>targetLength information should be read from the input, not from a supplied target
* file in compact format.</li>
* </ol>
* <p/>
* False by default when constructed, overidden by configure with default
* configuration=true when run as a mode on the command line, set to false
* explictly each time another Goby mode needs to import internally the result
* of a Goby search.
*/
protected boolean thirdPartyInput = true;
protected int smallestQueryIndex;
protected int largestQueryIndex = -1;
/**
* This method is deprecated, store read lengths directly into the alignment entry instead.
*
* @return
*/
@Deprecated
protected int[] createReadLengthArray() {
return new int[largestQueryIndex - smallestQueryIndex + 1];
}
/**
* Scan.
*
* @param readIndexFilter
* @param writer
* @param targetIds
* @param tmhWriter
* @return number of alignment entries written
* @throws IOException error parsing
*/
protected abstract int scan(ReadSet readIndexFilter, IndexedIdentifier targetIds,
AlignmentWriter writer,
AlignmentTooManyHitsWriter tmhWriter) throws IOException;
/**
* Configure.
*
* @param args command line arguments
* @return this object for chaining
* @throws java.io.IOException error parsing
* @throws com.martiansoftware.jsap.JSAPException
* error parsing
*/
@Override
public AbstractCommandLineMode configure(final String[] args) throws IOException, JSAPException {
//
final JSAPResult jsapResult = parseJsapArguments(args);
inputFile = jsapResult.getString("input");
outputFile = jsapResult.getString("output");
queryReadIdsFilename = jsapResult.getString("query-reads-ids");
targetReferenceIdsFilename = jsapResult.getString("target-reference-ids");
propagateQueryIds = jsapResult.getBoolean("propagate-query-ids");
propagateTargetIds = jsapResult.getBoolean("propagate-target-ids");
readIndexFilterFile = jsapResult.getFile("read-index-filter");
mParameter = jsapResult.getInt("ambiguity-threshold");
qualityFilterParameters = jsapResult.getString("quality-filter-parameters");
thirdPartyInput = jsapResult.getBoolean("third-party-input");
return this;
}
/**
* Run the alignment-to-compact mode.
*
* @throws java.io.IOException error reading / writing
*/
@Override
public void execute() throws IOException {
// read target/query identifier lookup table, and initialize output alignment
// file with this information
final TransferIds transferIds = new TransferIds().invoke();
final ReadSet readIndexFilter = transferIds.getReadIndexFilter();
final AlignmentWriterImpl writer = transferIds.getWriter();
targetIds.clear();
targetIds.putAll(transferIds.getTargetIds());
// initialize too-many-hits output file
final AlignmentTooManyHitsWriter tmhWriter =
new AlignmentTooManyHitsWriter(outputFile, mParameter);
try {
// initialize numberOfReads
if (numberOfReads < 0 && transferIds.numberOfReads != 0) {
numberOfReads = transferIds.numberOfReads;
}
if (numberOfReads <= 0) {
numberOfReads = numberOfReadsFromCommandLine;
}
if (numberOfReads < 0) {
System.err.println("Cannot determine number of reads. Must set property or provide reads file with -q");
return;
}
// initialize quality filter
qualityFilter = new PercentMismatchesQualityFilter();
qualityFilter.setParameters(qualityFilterParameters);
final int numAligns = scan(readIndexFilter, targetIds, writer, tmhWriter);
System.out.println("Number of alignments written: " + numAligns);
if (propagateQueryIds && !queryIds.isEmpty()) {
// we collected query ids, let's write them to the header:
writer.setQueryIdentifiers(queryIds);
}
if (propagateTargetIds && !targetIds.isEmpty()) {
// we collected target ids, let's write them to the header:
writer.setTargetIdentifiers(targetIds);
}
writer.setSmallestSplitQueryIndex(smallestQueryIndex);
assert largestQueryIndex > -1 : "largestQueryIndex must be set (set with --number-of-reads when running from command line).";
writer.setLargestSplitQueryIndex(largestQueryIndex);
} finally {
writer.close();
tmhWriter.close();
}
}
protected void evaluateStatistics(final AlignedSequence reference, final AlignedSequence query, final AlignmentStats stats) {
final MutableString queryAligned = query.alignment;
final MutableString targetAligned = reference.alignment;
// assert reference.alignedLength == query.alignedLength :"aligned length differ for queryIndex="+query.sequenceIdentifier;
final int length = Math.max(query.alignedLength, reference.alignedLength);
int numIndels = 0;
int numMismatches = 0;
for (int i = 0; i < length; i++) {
final char queryBase = queryAligned.charAt(i);
final char targetBase = targetAligned.charAt(i);
if (queryBase == '-' && targetBase != '-' || queryBase != '-' && targetBase == '-') {
numIndels++;
}
if (queryBase != '-' && targetBase != '-' && queryBase != targetBase) {
numMismatches++;
}
}
stats.numberOfIndels = numIndels;
stats.numberOfMismatches = numMismatches;
}
public void setInputFile(final String inputFile) {
this.inputFile = inputFile;
}
public void setOutputFile(final String outputFile) {
this.outputFile = outputFile;
}
public String getOutputFile() {
return outputFile;
}
public void setQueryReadIdsFilename(final String queryReadIdsFilename) {
this.queryReadIdsFilename = queryReadIdsFilename;
}
public void setTargetReferenceIdsFilename(final String targetReferenceIdsFilename) {
this.targetReferenceIdsFilename = targetReferenceIdsFilename;
}
public void setPropagateTargetIds(final boolean propagateTargetIds) {
this.propagateTargetIds = propagateTargetIds;
}
public void setPropagateQueryIds(final boolean propagateQueryIds) {
this.propagateQueryIds = propagateQueryIds;
}
public void setAmbiguityThreshold(final int mParameter) {
this.mParameter = mParameter;
}
public void setQualityFilterParameters(final String qualityFilterParameters) {
this.qualityFilterParameters = qualityFilterParameters;
}
public void setNumberOfReads(final int numberOfReads) {
this.numberOfReads = numberOfReads;
}
public void setThirdPartyInput(final boolean thirdPartyInput) {
this.thirdPartyInput = thirdPartyInput;
}
public void setSmallestQueryIndex(final int smallestQueryIndex) {
this.smallestQueryIndex = smallestQueryIndex;
}
public void setLargestQueryIndex(final int largestQueryIndex) {
this.largestQueryIndex = largestQueryIndex;
}
public void setNumberOfQuerySequences(final int numberOfReads) {
this.numberOfReadsFromCommandLine = numberOfReads;
}
public static int getTargetIndex(final IndexedIdentifier targetIds,
final CharSequence targetIdentifier,
final boolean thirdPartyInput) {
int targetIndex = -1;
try {
if (thirdPartyInput) {
targetIndex = targetIds.registerIdentifier(new MutableString(targetIdentifier));
} else {
targetIndex = Integer.parseInt(targetIdentifier.toString());
}
} catch (NumberFormatException e) {
if (targetIds != null) {
final Integer object = targetIds.get(targetIdentifier);
if (object == null) {
LOG.warn("Input file contains a target id that is not defined in the target compact reads: " + targetIdentifier);
targetIndex = targetIds.registerIdentifier(new MutableString(targetIdentifier));
} else {
targetIndex = object;
}
if (targetIndex == -1) {
System.out.println("Cannot convert reference identifier to index. " + targetIdentifier);
System.exit(1);
}
}
}
return targetIndex;
}
/**
* Compare read and reference sequences to determine sequence variations. The variations found
* are appended to the alignment entry builder.
*
* @param currentEntry alignment entry where variations will be stored.
* @param alignmentLength length of the sequence alignment (common length of reference and read sequences)
* @param referenceSequence The reference sequence
* @param readSequence The read sequence
* @param queryLength
* @param baseQualities ASCII encoded, remove 33 to get Phred quality score (see http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf)
*/
public static void extractSequenceVariations(final Alignments.AlignmentEntry.Builder currentEntry, final int alignmentLength,
final MutableString referenceSequence,
final MutableString readSequence,
final int readStartPosition,
final int queryLength, final boolean reverseStrand,
byte[] baseQualities) {
// System.out.printf("Extracting variations from %n%s%n%s%n",
// referenceSequence, readSequence);
final MutableString from = new MutableString();
final MutableString to = new MutableString();
ByteArrayList mutatedQualityScores=new ByteArrayList();
int variationPosition = Integer.MAX_VALUE;
int minLength = Math.min(referenceSequence.length(), readSequence.length());
minLength = Math.min(alignmentLength, minLength);
// will record the number of gaps in the read, up to the variation position. We need to
// subtract this number from the position to obtain the read index.
int readIndexAdjustment = 0;
int newAdjustment = 0;
for (int position = 0; position < minLength; ++position) {
final char referenceBase = referenceSequence.charAt(position);
final char queryBase = readSequence.charAt(position);
if (referenceBase != queryBase) {
from.append(referenceBase);
to.append(queryBase);
variationPosition = Math.min(variationPosition, position);
if (queryBase == '-') {
++newAdjustment;
}
mutatedQualityScores.add(baseQualities[position]);
} else {
appendNewSequenceVariation(currentEntry, from, to, variationPosition, readStartPosition, queryLength,
reverseStrand, readIndexAdjustment, mutatedQualityScores.toByteArray());
variationPosition = Integer.MAX_VALUE;
from.setLength(0);
to.setLength(0);
readIndexAdjustment = newAdjustment;
}
}
appendNewSequenceVariation(currentEntry, from, to, variationPosition, readStartPosition, queryLength, reverseStrand, readIndexAdjustment, mutatedQualityScores.toByteArray());
}
static WarningCounter noQualScoresWarning=new WarningCounter(10);
static WarningCounter sequenceVariationWarning=new WarningCounter(10);
/**
* @param currentEntry
* @param from
* @param to
* @param variationPosition
* @param readStartPosition
* @param queryLength
* @param reverseStrand
* @param readIndexAdjustment
* @param baseQualities ASCII encoded, remove 33 to get Phred quality score.
*/
private static void appendNewSequenceVariation(final Alignments.AlignmentEntry.Builder currentEntry,
final MutableString from,
final MutableString to,
final int variationPosition,
final int readStartPosition,
final int queryLength,
final boolean reverseStrand,
final int readIndexAdjustment,
byte[] baseQualities) {
if (variationPosition != Integer.MAX_VALUE) {
final Alignments.SequenceVariation.Builder sequenceVariation =
Alignments.SequenceVariation.newBuilder();
sequenceVariation.setFrom(from.toString());
sequenceVariation.setTo(to.toString());
sequenceVariation.setPosition(variationPosition + 1); // positions start at 1
// calculate the readIndex, taking strand and query length into consideration:
final int readIndex = (reverseStrand ? (queryLength - (variationPosition - readIndexAdjustment) - readStartPosition) :
variationPosition - readIndexAdjustment + readStartPosition);
if (readIndex > queryLength) {
assert readIndex <= queryLength : String.format(" readIndex %d must be smaller than read length %d .",
readIndex,
queryLength);
sequenceVariationWarning.warn(LOG,"Ignoring sequence variations for a read since readIndex %d must be smaller than read length %d. query index=%d reference index=%d%n", readIndex,
queryLength, currentEntry.getQueryIndex(),
currentEntry.getTargetIndex());
//System.exit(1);
return;
}
int correctedReadIndex = readIndex + (reverseStrand ? 0 : 1); // positions start at 1
sequenceVariation.setReadIndex(correctedReadIndex);
if (baseQualities != null) { // transfer read qualities for this sequence variation:
sequenceVariation.setToQuality(ByteString.copyFrom(baseQualities));
}
// do not offset if the match is in the reverse strand, since subtracting from the length takes care of offseting already.
// System.out.printf("Appending variation: %d %s/%s ", variationPosition, from, to);
currentEntry.addSequenceVariations(sequenceVariation);
// reset since they are used:
from.setLength(0);
to.setLength(0);
}
}
public class TransferIds {
private ReadSet readIndexFilter;
private AlignmentWriterImpl writer;
private IndexedIdentifier targetIds;
public int numberOfReads = -1;
public int numberOfReadsForSplit;
private int numberOfTargets;
public ReadSet getReadIndexFilter() {
return readIndexFilter;
}
public AlignmentWriterImpl getWriter() {
return writer;
}
public IndexedIdentifier getTargetIds() {
return targetIds;
}
/**
* Postcondition: output Ids.size() == maximumSequenceIndex + 1.
*/
private ObjectArrayList<String> processIds(final String idsFilename) throws FileNotFoundException {
final ObjectArrayList<String> ids = new ObjectArrayList<String>(500000);
int minSequenceIndex = Integer.MAX_VALUE;
int maxSequenceIndex = Integer.MIN_VALUE;
ReadsReader idsReader = null;
try {
idsReader = new ReadsReader(new FileInputStream(idsFilename));
boolean atLeastOneId = false;
ids.size(500000);
while (idsReader.hasNext()) {
final Reads.ReadEntry readEntry = idsReader.next();
final int readIndex = readEntry.getReadIndex();
if (readEntry.hasReadIdentifier()) {
// resize as necessary:
if (readIndex >= ids.size()) {
final double newSize = ids.size() * 1.5;
// System.out.println("resizing to " + newSize);
ids.size((int) newSize);
}
// set element:
ids.set(readIndex, readEntry.getReadIdentifier());
atLeastOneId = true;
}
minSequenceIndex = Math.min(minSequenceIndex, readIndex);
maxSequenceIndex = Math.max(maxSequenceIndex, readIndex);
}
} finally {
if (idsReader != null) {
try {
idsReader.close();
} catch (IOException e) {
LOG.warn("Error closing " + idsFilename, e);
}
}
}
ids.size(maxSequenceIndex + 1);
this.numberOfReadsForSplit = (maxSequenceIndex - minSequenceIndex) + 1;
ids.trim();
assert ids.size() == maxSequenceIndex + 1;
return ids;
}
public AbstractAlignmentToCompactMode.TransferIds invoke() throws IOException {
// setup multiplicity set:
readIndexFilter = new ReadSet();
if (readIndexFilterFile == null) {
readIndexFilter = null;
} else {
readIndexFilter.load(readIndexFilterFile);
}
writer = new AlignmentWriterImpl(outputFile);
targetIds = new IndexedIdentifier();
// first write reference ids to compact header, if these ids are provided on the command line:
if (targetReferenceIdsFilename != null) {
System.out.println("Scanning target file..");
// read reference ids from file
final ObjectArrayList<String> ids = processIds(targetReferenceIdsFilename);
this.numberOfTargets = ids.size();
System.out.println("Target file had " + this.numberOfTargets + " entries.");
// write ids to header
writer.setNumTargets(this.numberOfTargets);
if (this.numberOfTargets > 0 && propagateTargetIds) {
writer.setTargetIdentifiersArray(ids.toArray(new String[ids.size()]));
System.out.println("Wrote " + ids.size() + " target ids to alignment header.");
} else {
System.out.println("Target ids are not propagated to output header.");
}
for (int index = 0; index < ids.size(); index++) {
final String id = ids.get(index);
if (id != null) {
targetIds.put(new MutableString(id), index);
}
}
}
// write query/read ids to compact header, if provided as well:
if (queryReadIdsFilename != null) {
// read read ids from file
System.out.println("Scanning query file..");
final ObjectArrayList<String> ids = processIds(queryReadIdsFilename);
this.numberOfReads = ids.size();
// System.out.println("Query file had " + this.numberOfReads + " entries.");
for (final String id : ids) {
if (id != null) {
queryIds.registerIdentifier(new MutableString(id));
}
}
// write ids to header
writer.setNumQueries(this.numberOfReadsForSplit);
if (this.numberOfReads > 0 && propagateQueryIds) {
writer.setQueryIdentifiersArray(ids.toArray(new String[ids.size()]));
System.out.println("Wrote " + ids.size() + " query ids to alignment header.");
} else {
System.out.println("Query ids are not propagated to output header.");
}
}
return this;
}
}
}
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