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Some walkers for printing FASTA of reference for bed ROD, and "inverting" a bed file (finding regions not covered in bed) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5554 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-04-01 21:13:51 +00:00
parent 73f0610abf
commit 27bfec785e
3 changed files with 267 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
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@ -44,6 +44,10 @@ public class FastaSequence {
sequenceCounter++; sequenceCounter++;
} }
public long getCurrentCount() {
return sequenceCounter;
}
public String getCurrentID() { public String getCurrentID() {
return String.valueOf(sequenceCounter); return String.valueOf(sequenceCounter);
} }

122
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/PrintIntervalsNotInBedWalker.java 100644
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@ -0,0 +1,122 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.oneoffprojects.walkers.CNV;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.PrintStream;
import java.util.List;
/**
* Walks along reference and prints intervals of sequence not covered in ANY interval in "intervals" ROD.
*/
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = PrintIntervalsNotInBedWalker.INTERVALS_ROD_NAME, type = ReferenceOrderedDatum.class)})
@By(DataSource.REFERENCE) // So that we will actually enter loci with no ROD on them
public class PrintIntervalsNotInBedWalker extends RodWalker<Integer, Integer> {
@Output
protected PrintStream out;
public final static String INTERVALS_ROD_NAME = "intervals";
private GenomeLoc waitingInterval = null;
public void initialize() {
}
public boolean generateExtendedEvents() {
return false;
}
public Integer reduceInit() {
return 0;
}
/**
* @param tracker the meta-data tracker
* @param ref the reference base
* @param context the context for the given locus
* @return number of intervals printed.
*/
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null)
return null;
GenomeLoc curLoc = ref.getLocus();
int curPos = curLoc.getStart();
int printed = 0;
List<GATKFeature> intervals = tracker.getGATKFeatureMetaData(INTERVALS_ROD_NAME, true);
if (intervals.isEmpty()) {
if (waitingInterval != null && curLoc.compareContigs(waitingInterval) == 0 && curPos == waitingInterval.getStop() + 1) {
waitingInterval = getToolkit().getGenomeLocParser().setStop(waitingInterval, curPos);
}
else {
printed += printWaitingIntervalAsBed();
waitingInterval = ref.getLocus().clone();
}
}
else {
printed += printWaitingIntervalAsBed();
}
return printed;
}
public Integer reduce(Integer add, Integer runningCount) {
if (add == null)
add = 0;
return runningCount + add;
}
/**
* @param result the genes found in each interval.
*/
public void onTraversalDone(Integer result) {
result += printWaitingIntervalAsBed();
System.out.println("Printed out " + result + " intervals.");
}
private int printWaitingIntervalAsBed() {
if (waitingInterval == null)
return 0;
out.println(waitingInterval.getContig() + "\t" + (waitingInterval.getStart() - 1) + "\t" + waitingInterval.getStop());
waitingInterval = null;
return 1;
}
}

141
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/ReferenceFASTAforBedIntervalsWalker.java 100755
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@ -0,0 +1,141 @@
/*
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.oneoffprojects.walkers.CNV;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.fasta.FastaSequence;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* Walks along reference and prints the reference sequence (as FASTA) for the BED file intervals ("intervals" ROD).
*/
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = ReferenceFASTAforBedIntervalsWalker.INTERVALS_ROD_NAME, type = ReferenceOrderedDatum.class)})
public class ReferenceFASTAforBedIntervalsWalker extends RodWalker<Integer, Integer> {
@Output
protected PrintStream out;
public final static String INTERVALS_ROD_NAME = "intervals";
private Map<GenomeLoc, FastaSequence> intervalSequences;
private final static int LINE_WIDTH = 60;
public void initialize() {
this.intervalSequences = new HashMap<GenomeLoc, FastaSequence>();
}
public boolean generateExtendedEvents() {
return false;
}
public Integer reduceInit() {
return 0;
}
/**
* @param tracker the meta-data tracker
* @param ref the reference base
* @param context the context for the given locus
* @return number of interval sequences printed
*/
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null)
return null;
GenomeLoc curLoc = ref.getLocus();
int curPos = curLoc.getStart();
int entries = 0;
List<GATKFeature> intervals = tracker.getGATKFeatureMetaData(INTERVALS_ROD_NAME, true);
for (GATKFeature interval : intervals) {
GenomeLoc loc = interval.getLocation();
/* TODO: note that an interval may actually start BEFORE here, but not be covered, but would need to cache the remappings
of origLoc -> newLoc, and then setName(newLoc.toString()) */
FastaSequence seq = null;
if (loc.getStart() == curPos) { // at the start of this interval:
seq = new FastaSequence(out, LINE_WIDTH, false);
seq.setName(loc.toString());
intervalSequences.put(loc, seq);
}
else {
seq = intervalSequences.get(loc);
}
seq.append(String.valueOf((char) ref.getBase()));
if (loc.getStop() == curPos) { // at the end of this interval:
intervalSequences.remove(loc);
seq.flush();
entries++;
}
}
return entries;
}
public Integer reduce(Integer add, Integer runningCount) {
if (add == null)
add = 0;
return runningCount + add;
}
/**
* @param result the genes found in each interval.
*/
public void onTraversalDone(Integer result) {
result += intervalSequences.size();
for (Map.Entry<GenomeLoc, FastaSequence> locSeqEntry : intervalSequences.entrySet()) {
GenomeLoc interval = locSeqEntry.getKey();
FastaSequence seq = locSeqEntry.getValue();
int actualStop = interval.getStart() + (int)seq.getCurrentCount() - 1;
GenomeLoc actualInterval = getToolkit().getGenomeLocParser().setStop(interval, actualStop);
seq.setName(actualInterval.toString());
seq.flush();
}
System.out.println("Printed out " + result + " sequence entries.");
}
}