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GeneNamesIntervalWalker outputs all genes in each interval; walkers now require a ROD named "intervals" 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5254 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-02-16 19:58:09 +00:00
parent 50c870cfce
commit 6e291820d3
3 changed files with 169 additions and 12 deletions
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16
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/GCcontentIntervalWalker.java
View File

@ -24,13 +24,9 @@
package org.broadinstitute.sting.oneoffprojects.walkers.CNV;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.Argument;
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.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
@ -43,15 +39,17 @@ import java.io.PrintStream;
import java.util.*;
/**
* Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites.
* Walks along reference and calculates the GC content for each interval defined in "intervals" ROD.
*/
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = GCcontentIntervalWalker.INTERVALS_ROD_NAME, type = ReferenceOrderedDatum.class)})
public class GCcontentIntervalWalker extends RodWalker<GCcounter, GCcounter> {
@Output
protected PrintStream out;
public final static String INTERVALS_ROD_NAME = "intervals";
public boolean isReduceByInterval() {
return true;
}
@ -77,9 +75,9 @@ public class GCcontentIntervalWalker extends RodWalker<GCcounter, GCcounter> {
if (tracker == null)
return null;
List<GATKFeature> interval = tracker.getGATKFeatureMetaData("intervals", true);
List<GATKFeature> interval = tracker.getGATKFeatureMetaData(INTERVALS_ROD_NAME, true);
if (interval.size() != 1) {
String error = "At " + ref.getLocus() + " : Must provide a track named 'intervals' with exactly ONE interval per locus in -L argument!";
String error = "At " + ref.getLocus() + " : Must provide a track named '"+ INTERVALS_ROD_NAME +"' with exactly ONE interval per locus in -L argument!";
if (interval.size() < 1)
throw new UserException(error);
else // interval.size() > 1
@ -102,7 +100,7 @@ public class GCcontentIntervalWalker extends RodWalker<GCcounter, GCcounter> {
}
/**
* @param result the number of reads and VariantContexts seen.
* @param result the GC content observed.
*/
public void onTraversalDone(GCcounter result) {
if (result.loc == null)

157
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CNV/GeneNamesIntervalWalker.java 100755
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@ -0,0 +1,157 @@
/*
* 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.features.annotator.AnnotatorInputTableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.PrintStream;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
/**
* Walks along reference and calculates the genes (from "" ROD) for each interval defined in "intervals" ROD.
*/
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = GeneNamesIntervalWalker.REFSEQ_ROD_NAME, type = AnnotatorInputTableFeature.class), @RMD(name = GeneNamesIntervalWalker.INTERVALS_ROD_NAME, type = ReferenceOrderedDatum.class)})
public class GeneNamesIntervalWalker extends RodWalker<GeneNames, GeneNames> {
@Output
protected PrintStream out;
public final static String REFSEQ_ROD_NAME = "refseq";
public final static String INTERVALS_ROD_NAME = "intervals";
public final static String REFSEQ_NAME2 = "name2";
public boolean isReduceByInterval() {
return true;
}
public void initialize() {
}
public boolean generateExtendedEvents() {
return false;
}
public GeneNames reduceInit() {
return new GeneNames();
}
/**
* @param tracker the meta-data tracker
* @param ref the reference base
* @param context the context for the given locus
* @return statistics of and list of all phased VariantContexts and their base pileup that have gone out of cacheWindow range.
*/
public GeneNames map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null)
return null;
List<GATKFeature> interval = tracker.getGATKFeatureMetaData(INTERVALS_ROD_NAME, true);
if (interval.size() != 1) {
String error = "At " + ref.getLocus() + " : Must provide a track named '"+ INTERVALS_ROD_NAME +"' with exactly ONE interval per locus in -L argument!";
if (interval.size() < 1)
throw new UserException(error);
else // interval.size() > 1
logger.warn(error);
}
GenomeLoc curInterval = interval.get(0).getLocation();
GeneNames names = new GeneNames();
names.addGenes(tracker.getReferenceMetaData(REFSEQ_ROD_NAME));
names.loc = curInterval;
return names;
}
public GeneNames reduce(GeneNames add, GeneNames runningCount) {
if (add == null)
add = new GeneNames();
return runningCount.addIn(add);
}
/**
* @param result the genes in the interval.
*/
public void onTraversalDone(GeneNames result) {
if (result.loc == null)
return;
out.println(result.loc + "\t" + result);
}
}
class GeneNames {
public Set<String> geneNames;
public GenomeLoc loc;
public GeneNames() {
this.geneNames = new HashSet<String>();
this.loc = null;
}
public GeneNames addIn(GeneNames other) {
this.geneNames.addAll(other.geneNames);
if (other.loc != null && this.loc == null)
this.loc = other.loc;
return this;
}
public void addGenes(List<Object> refSeqRODs) {
for (Object refSeqObject : refSeqRODs) {
AnnotatorInputTableFeature refSeqAnnotation = (AnnotatorInputTableFeature) refSeqObject;
if (refSeqAnnotation.containsColumnName(GeneNamesIntervalWalker.REFSEQ_NAME2))
geneNames.add(refSeqAnnotation.getColumnValue(GeneNamesIntervalWalker.REFSEQ_NAME2));
}
}
public String toString() {
if (geneNames.isEmpty())
return ".";
StringBuilder sb = new StringBuilder();
for (String gene : geneNames)
sb.append(gene).append(";");
return sb.toString();
}
}

8
java/src/org/broadinstitute/sting/oneoffprojects/walkers/phasing/CountHetPhasingInIntervalWalker.java
View File

@ -45,7 +45,7 @@ import java.util.*;
* Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites.
*/
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE}, referenceMetaData = @RMD(name = "variant", type = ReferenceOrderedDatum.class))
@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = "variant", type = ReferenceOrderedDatum.class), @RMD(name = CountHetPhasingInIntervalWalker.INTERVALS_ROD_NAME, type = ReferenceOrderedDatum.class)})
@ReadFilters({ZeroMappingQualityReadFilter.class})
// Filter out all reads with zero mapping quality
@ -63,6 +63,8 @@ public class CountHetPhasingInIntervalWalker extends RodWalker<Integer, Integer>
@Argument(fullName = "perIntervalOut", shortName = "perIntervalOut", doc = "File to which to write per-sample, per-interval phased het statistics", required = false)
protected PrintStream perIntervalOut = null;
public final static String INTERVALS_ROD_NAME = "intervals";
public void initialize() {
rodNames = new LinkedList<String>();
rodNames.add("variant");
@ -90,9 +92,9 @@ public class CountHetPhasingInIntervalWalker extends RodWalker<Integer, Integer>
int processed = 1;
List<GATKFeature> interval = tracker.getGATKFeatureMetaData("intervals", true);
List<GATKFeature> interval = tracker.getGATKFeatureMetaData(INTERVALS_ROD_NAME, true);
if (interval.size() != 1) {
String error = "At " + ref.getLocus() + " : Must provide a track named 'intervals' with exactly ONE interval per locus in -L argument!";
String error = "At " + ref.getLocus() + " : Must provide a track named '"+ INTERVALS_ROD_NAME +"' with exactly ONE interval per locus in -L argument!";
if (interval.size() < 1)
throw new UserException(error);
else // interval.size() > 1