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
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@ -44,6 +44,10 @@ public class FastaSequence {
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sequenceCounter++;
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}
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public long getCurrentCount() {
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return sequenceCounter;
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}
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public String getCurrentID() {
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return String.valueOf(sequenceCounter);
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}
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@ -0,0 +1,122 @@
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/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.walkers.CNV;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import java.io.PrintStream;
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import java.util.List;
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/**
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* Walks along reference and prints intervals of sequence not covered in ANY interval in "intervals" ROD.
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = PrintIntervalsNotInBedWalker.INTERVALS_ROD_NAME, type = ReferenceOrderedDatum.class)})
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@By(DataSource.REFERENCE) // So that we will actually enter loci with no ROD on them
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public class PrintIntervalsNotInBedWalker extends RodWalker<Integer, Integer> {
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@Output
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protected PrintStream out;
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public final static String INTERVALS_ROD_NAME = "intervals";
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private GenomeLoc waitingInterval = null;
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public void initialize() {
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}
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public boolean generateExtendedEvents() {
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return false;
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}
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public Integer reduceInit() {
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return 0;
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}
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/**
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return number of intervals printed.
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (tracker == null)
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return null;
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GenomeLoc curLoc = ref.getLocus();
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int curPos = curLoc.getStart();
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int printed = 0;
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List<GATKFeature> intervals = tracker.getGATKFeatureMetaData(INTERVALS_ROD_NAME, true);
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if (intervals.isEmpty()) {
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if (waitingInterval != null && curLoc.compareContigs(waitingInterval) == 0 && curPos == waitingInterval.getStop() + 1) {
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waitingInterval = getToolkit().getGenomeLocParser().setStop(waitingInterval, curPos);
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}
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else {
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printed += printWaitingIntervalAsBed();
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waitingInterval = ref.getLocus().clone();
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}
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}
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else {
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printed += printWaitingIntervalAsBed();
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}
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return printed;
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}
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public Integer reduce(Integer add, Integer runningCount) {
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if (add == null)
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add = 0;
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return runningCount + add;
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}
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/**
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* @param result the genes found in each interval.
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*/
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public void onTraversalDone(Integer result) {
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result += printWaitingIntervalAsBed();
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System.out.println("Printed out " + result + " intervals.");
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}
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private int printWaitingIntervalAsBed() {
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if (waitingInterval == null)
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return 0;
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out.println(waitingInterval.getContig() + "\t" + (waitingInterval.getStart() - 1) + "\t" + waitingInterval.getStop());
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waitingInterval = null;
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return 1;
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}
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}
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@ -0,0 +1,141 @@
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/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.walkers.CNV;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.walkers.fasta.FastaSequence;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.collections.Pair;
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import java.io.PrintStream;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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/**
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* Walks along reference and prints the reference sequence (as FASTA) for the BED file intervals ("intervals" ROD).
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = ReferenceFASTAforBedIntervalsWalker.INTERVALS_ROD_NAME, type = ReferenceOrderedDatum.class)})
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public class ReferenceFASTAforBedIntervalsWalker extends RodWalker<Integer, Integer> {
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@Output
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protected PrintStream out;
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public final static String INTERVALS_ROD_NAME = "intervals";
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private Map<GenomeLoc, FastaSequence> intervalSequences;
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private final static int LINE_WIDTH = 60;
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public void initialize() {
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this.intervalSequences = new HashMap<GenomeLoc, FastaSequence>();
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}
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public boolean generateExtendedEvents() {
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return false;
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}
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public Integer reduceInit() {
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return 0;
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}
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/**
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return number of interval sequences printed
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (tracker == null)
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return null;
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GenomeLoc curLoc = ref.getLocus();
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int curPos = curLoc.getStart();
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int entries = 0;
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List<GATKFeature> intervals = tracker.getGATKFeatureMetaData(INTERVALS_ROD_NAME, true);
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for (GATKFeature interval : intervals) {
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GenomeLoc loc = interval.getLocation();
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/* TODO: note that an interval may actually start BEFORE here, but not be covered, but would need to cache the remappings
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of origLoc -> newLoc, and then setName(newLoc.toString()) */
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FastaSequence seq = null;
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if (loc.getStart() == curPos) { // at the start of this interval:
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seq = new FastaSequence(out, LINE_WIDTH, false);
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seq.setName(loc.toString());
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intervalSequences.put(loc, seq);
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}
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else {
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seq = intervalSequences.get(loc);
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}
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seq.append(String.valueOf((char) ref.getBase()));
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if (loc.getStop() == curPos) { // at the end of this interval:
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intervalSequences.remove(loc);
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seq.flush();
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entries++;
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}
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}
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return entries;
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}
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public Integer reduce(Integer add, Integer runningCount) {
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if (add == null)
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add = 0;
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return runningCount + add;
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}
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/**
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* @param result the genes found in each interval.
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*/
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public void onTraversalDone(Integer result) {
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result += intervalSequences.size();
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for (Map.Entry<GenomeLoc, FastaSequence> locSeqEntry : intervalSequences.entrySet()) {
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GenomeLoc interval = locSeqEntry.getKey();
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FastaSequence seq = locSeqEntry.getValue();
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int actualStop = interval.getStart() + (int)seq.getCurrentCount() - 1;
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GenomeLoc actualInterval = getToolkit().getGenomeLocParser().setStop(interval, actualStop);
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seq.setName(actualInterval.toString());
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seq.flush();
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}
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System.out.println("Printed out " + result + " sequence entries.");
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}
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}
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