Merge pull request #886 from broadinstitute/ami-RNA-ASEtools-march2015
Ami RNA ASE tools
This commit is contained in:
amilev
commit
244dbe8634
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@ -183,7 +183,7 @@ public class FisherStrand extends StrandBiasTest implements StandardAnnotation,
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return list;
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return list;
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}
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}
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private Double pValueForContingencyTable(int[][] originalTable) {
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public static Double pValueForContingencyTable(int[][] originalTable) {
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final int[][] normalizedTable = normalizeContingencyTable(originalTable);
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final int[][] normalizedTable = normalizeContingencyTable(originalTable);
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int[][] table = copyContingencyTable(normalizedTable);
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int[][] table = copyContingencyTable(normalizedTable);
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@ -0,0 +1,286 @@
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/*
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* Copyright (c) 2012 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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*
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.gatk.tools.walkers.rnaseq;
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import htsjdk.variant.variantcontext.VariantContext;
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import org.broadinstitute.gatk.engine.filters.DuplicateReadFilter;
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import org.broadinstitute.gatk.engine.walkers.DisabledReadFilters;
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import org.broadinstitute.gatk.engine.walkers.Downsample;
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import org.broadinstitute.gatk.engine.walkers.LocusWalker;
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import org.broadinstitute.gatk.tools.walkers.coverage.CoverageUtils;
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import org.broadinstitute.gatk.utils.commandline.*;
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import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
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import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
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import org.broadinstitute.gatk.utils.downsampling.DownsampleType;
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import org.broadinstitute.gatk.utils.exceptions.UserException;
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import org.broadinstitute.gatk.utils.pileup.PileupElement;
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import org.broadinstitute.gatk.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
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import java.io.PrintStream;
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import java.util.List;
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/**
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* Calculated allele counts in specific loci, to allow allele specific expression analysis.
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*
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* <p>
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* Calculated allele counts in specific loci after filtering based on mapping quality, base quality, depth of coverage, overlapping paired reads and deletion on the position.
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* All thresholds and option can be set as command line arguments.
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* The output of this tool is a tab delimited txt file, compatible with Mamba, a downstream tool (http://www.well.ox.ac.uk/~rivas/mamba/).
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* A user can use -drf DuplicateRead to allow the tool to count also duplicated reads (a useful option for RNAseq data tools)
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* </p>
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*
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* <h3>Input</h3>
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* <p>
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* BAM files (with proper headers) to be analyzed for ASE * </p>
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* <p>
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* a VCF file with specific sites to process
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* </p>
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* </p></p>
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* <h3>Output</h3>
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* <p>
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* Table (tab delimited file) with the specific allele counts
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* </p>
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*
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* <h3>Examples</h3>
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* <pre>
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* java -jar GenomeAnalysisTK.jar \
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* -R ref.fasta \
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* -T ASEReadCounter \
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* -o file_name \
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* -I input.bam \
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* -sites sites.vcf
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* -U ALLOW_N_CIGAR_READS
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* [-minDepth 10] \
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* [--minMappingQuality 10] \
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* [--minBaseQuality 2]
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* [-drf DuplicateRead]
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* </pre>
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*/
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@Downsample(by = DownsampleType.BY_SAMPLE, toCoverage = 10000)
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//@DisabledReadFilters({DuplicateReadFilter.class}) //currently can be disabled using the command line argument -drf DuplicateRead
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public class ASEReadCounter extends LocusWalker<String, Integer> {
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@Output
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public PrintStream out;
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@Input (fullName = "sitesVCFFile",shortName = "sites")
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public RodBinding<VariantContext> sites;
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/**
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* Loci with total depth lower then this threshold will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
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*/
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@Argument(fullName = "minDepthOfNonFilteredBase", shortName = "minDepth", doc = "Minimum number of filtered-pass bases that we need to see for reporting this site", required = false, minValue = 0, maxValue = Integer.MAX_VALUE)
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public int minDepthOfNonFilteredBases = -1;
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/**
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* Reads with mapping quality values lower than this threshold will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
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*/
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@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth", required = false, minValue = 0, maxValue = Integer.MAX_VALUE)
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public int minMappingQuality = 0;
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/**
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* Bases with quality scores lower than this threshold will be skipped. This is set to -1 by default to disable the evaluation and ignore this threshold.
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*/
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@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth", required = false, minValue = 0, maxValue = Byte.MAX_VALUE)
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public byte minBaseQuality = 0;
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/**
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* There are few option to deal with an overlapping read pair.
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* COUNT_READS - Count all reads independently (even if from the same fragment).
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* COUNT_FRAGMENTS - Count all fragments (even if the reads that compose the fragment are not consistent at that base).
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* COUNT_FRAGMENTS_REQUIRE_SAME_BASEQUIRE_SAME_BASE - Count all fragments (but only if the reads that compose the fragment are consistent at that base).
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* defaults to COUNT_FRAGMENTS_REQUIRE_SAME_BASEQUIRE_SAME_BASE
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*/
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@Argument(fullName = "countOverlapReadsType", shortName = "overlap", doc = "How should overlapping reads from the same fragment be handled. Current options: COUNT_READS, COUNT_FRAGMENTS and COUNT_FRAGMENTS_REQUIRE_SAME_BASEQUIRE_SAME_BASE (default)", required = false)
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public CoverageUtils.CountPileupType countType = CoverageUtils.CountPileupType.COUNT_FRAGMENTS_REQUIRE_SAME_BASE;
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/**
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* Output file format (e.g. csv, table, rtable); defaults to r-readable table.
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*/
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@Argument(fullName = "outputFormat", doc = "The format of the output file, can be csv, table, rtable", required = false)
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public String outputFormat = "rtable";
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/**
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* Consider a spanning deletion as contributing to coverage. Also enables deletion counts in per-base output.
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*/
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@Advanced
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@Argument(fullName = "includeDeletions", shortName = "dels", doc = "Include information on deletions", required = false)
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public boolean includeDeletions = false;
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@Advanced
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@Argument(fullName = "ignoreDeletionSites", doc = "Ignore sites consisting only of deletions", required = false)
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public boolean ignoreDeletionSites = false;
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final String[] OUTPUT_FORMATS = {"table","rtable","csv"};
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public String separator = "\t";
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////////////////////////////////////////////////////////////////////////////////////
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// STANDARD WALKER METHODS
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////////////////////////////////////////////////////////////////////////////////////
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public boolean includeReadsWithDeletionAtLoci() { return includeDeletions && ! ignoreDeletionSites; }
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public void initialize() {
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// Check the output format
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boolean goodOutputFormat = false;
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for ( final String f : OUTPUT_FORMATS ) {
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goodOutputFormat = goodOutputFormat || f.equals(outputFormat);
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}
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if ( ! goodOutputFormat ) {
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throw new IllegalArgumentException("Improper output format. Can be one of table,rtable,csv. Was "+outputFormat);
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}
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if ( outputFormat.equals("csv") ) {
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separator = ",";
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}
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final String header = "contig"+separator+"position"+separator+"variantID"+separator+"refAllele"+separator+"altAllele"+separator+"refCount"+separator+"altCount"+separator+"totalCount"+separator+"lowMAPQDepth"+separator+"lowBaseQDepth"+separator+"rawDepth"+separator+"otherBases"+separator+"improperPairs";
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out.println(header);
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}
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@Override
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public String map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
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if ( tracker == null )
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return null;
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final String contig = context.getLocation().getContig();
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final long position = context.getPosition();
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final char refAllele = (char)ref.getBase();
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final List<VariantContext> VCs = tracker.getValues(sites, context.getLocation());
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if(VCs != null && VCs.size() > 1)
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throw new UserException("more then one variant context in position: "+contig+":"+position);
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if(VCs == null || VCs.size() == 0)
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return null;
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final VariantContext vc = VCs.get(0);
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if(!vc.isBiallelic()) {
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logger.warn("ignore site: cannot run ASE on non-biallelic sites: " + vc.toString());
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return null;
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}
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final char altAllele = (char)vc.getAlternateAllele(0).getBases()[0];
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final String siteID = vc.getID();
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final ReadBackedPileup pileup = filterPileup(context.getBasePileup(), countType, includeReadsWithDeletionAtLoci());
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// count up the depths of all and QC+ bases
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return calculateLineForSite(pileup, contig, position, siteID, refAllele, altAllele);
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}
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protected ReadBackedPileup filterPileup(final ReadBackedPileup originalPileup, final CoverageUtils.CountPileupType countType, final boolean includeDeletions){
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ReadBackedPileup pileupWithDeletions;
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if(countType.equals(CoverageUtils.CountPileupType.COUNT_FRAGMENTS_REQUIRE_SAME_BASE))
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pileupWithDeletions = originalPileup.getOverlappingFragmentFilteredPileup(true,true);
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else if(countType.equals(CoverageUtils.CountPileupType.COUNT_READS))
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pileupWithDeletions = originalPileup;
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else if(countType.equals(CoverageUtils.CountPileupType.COUNT_FRAGMENTS))
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pileupWithDeletions = originalPileup.getOverlappingFragmentFilteredPileup(false,true);
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else
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throw new UserException("Must use valid CountPileupType");
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return includeDeletions ? pileupWithDeletions: pileupWithDeletions.getPileupWithoutDeletions();
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}
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protected String calculateLineForSite(final ReadBackedPileup pileup, final String contig, final long position, final String siteID, final char refAllele, final char altAllele){
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int rawDepth = 0, lowBaseQDepth = 0, lowMAPQDepth = 0, refCount = 0, altCount = 0, totalNonFilteredCount = 0, otherBasesCount = 0, improperPairsCount = 0 ;
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for (final PileupElement base : pileup) {
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rawDepth++;
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if (!base.getRead().getProperPairFlag()){
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improperPairsCount++;
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continue;
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}
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if (base.getMappingQual() < minMappingQuality) {
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lowMAPQDepth++;
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continue;
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}
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if (base.getQual() < minBaseQuality) {
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lowBaseQDepth++;
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continue;
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}
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if(base.getBase() == refAllele)
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refCount++;
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else if(base.getBase() == altAllele)
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altCount++;
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else {
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otherBasesCount++;
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continue;
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}
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totalNonFilteredCount++;
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}
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if(totalNonFilteredCount < minDepthOfNonFilteredBases)
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return null;
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return contig +separator+
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position +separator+
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siteID +separator+
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refAllele +separator+
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altAllele +separator+
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refCount +separator+
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altCount +separator+
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totalNonFilteredCount +separator+
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lowMAPQDepth +separator+
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lowBaseQDepth +separator+
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rawDepth +separator+
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otherBasesCount +separator+
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improperPairsCount;
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}
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@Override
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public Integer reduceInit() {
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return 0;
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}
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@Override
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|
public Integer reduce(String results, Integer sum) {
|
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|
if(results!= null)
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|
out.println(results);
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return ++sum;
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}
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@Override
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public void onTraversalDone(Integer sum) {
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logger.info("Done processing "+sum+" loci");
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|
out.close();
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}
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}
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@ -0,0 +1,112 @@
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/*
|
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|
* Copyright (c) 2012 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.gatk.tools.walkers.rnaseq;
|
||||||
|
|
||||||
|
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
|
||||||
|
import org.testng.annotations.Test;
|
||||||
|
|
||||||
|
import java.util.Arrays;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Test all different parameters.
|
||||||
|
*/
|
||||||
|
public class ASEReadCounterIntegrationTest extends WalkerTest {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testASEReadCounterWithHighMQ() {
|
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|
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||||
|
"-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 60 -o %s -U ALLOW_N_CIGAR_READS", 1,
|
||||||
|
Arrays.asList("eec421405a4a570751821d158734020e"));
|
||||||
|
executeTest("test high mq with no read passing", spec);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testASEReadCounterWithLowMQ() {
|
||||||
|
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||||
|
"-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 1 -o %s -U ALLOW_N_CIGAR_READS", 1,
|
||||||
|
Arrays.asList("4f1144be0bb2c4adeae00625afd04cda"));
|
||||||
|
executeTest("test high mq with no read passing", spec);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testASEReadCounterWithLowMQNoDedup() {
|
||||||
|
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||||
|
"-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 10 -o %s -U ALLOW_N_CIGAR_READS -drf DuplicateRead", 1,
|
||||||
|
Arrays.asList("226021673310f28d6520d7f3cfe8cb4b"));
|
||||||
|
executeTest("test high mq with no read passing", spec);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testASEReadCounterWithHighMQLowBQ() {
|
||||||
|
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||||
|
"-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 60 -mbq 10 -o %s -U ALLOW_N_CIGAR_READS", 1,
|
||||||
|
Arrays.asList("f86bf14ca3a2cc0114d6a11de0cd9448"));
|
||||||
|
executeTest("test high mq with no read passing", spec);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testASEReadCounterWithCountOverlaps() {
|
||||||
|
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||||
|
"-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 60 -mbq 10 -o %s -U ALLOW_N_CIGAR_READS -overlap COUNT_FRAGMENTS", 1,
|
||||||
|
Arrays.asList("bfaeaaa8c000eca82f703225bf2257a1"));
|
||||||
|
executeTest("test high mq with no read passing", spec);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testASEReadCounterWithCountReads() {
|
||||||
|
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||||
|
"-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 60 -mbq 10 -o %s -U ALLOW_N_CIGAR_READS -overlap COUNT_READS", 1,
|
||||||
|
Arrays.asList("a9b420fd12a9162b31a48842c4081a1f"));
|
||||||
|
executeTest("test high mq with no read passing", spec);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testASEReadCounterMinDepth70() {
|
||||||
|
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||||
|
"-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 60 -mbq 10 -o %s -U ALLOW_N_CIGAR_READS -minDepth 70", 1,
|
||||||
|
Arrays.asList("79b99bc8a1c1c58ac860f79a11f93086"));
|
||||||
|
executeTest("test high mq with no read passing", spec);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testASEReadCounterFileFormat() {
|
||||||
|
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||||
|
"-T ASEReadCounter -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -sites "+privateTestDir +"NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 60 -mbq 10 -o %s -U ALLOW_N_CIGAR_READS --outputFormat csv", 1,
|
||||||
|
Arrays.asList("2c7c531018ab353e6874ee2da7980986"));
|
||||||
|
executeTest("test high mq with no read passing", spec);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue