Add band pass filtering activity profile
-- Based on the new incremental activity profile -- Unit Tested! Fixed a few bugs with the old band pass filter -- Expand IncrementalActivityProfileUnitTest to test the band pass filter as well for basic properties -- Add new UnitTest for BandPassIncrementalActivityProfile -- Added normalizeFromRealSpace to MathUtils -- Cleanup unused code in new activity profiles
This commit is contained in:
Mark DePristo
parent
eb60235dcd
commit
7fd27a5167
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@ -634,6 +634,30 @@ public class MathUtils {
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return normalizeFromLog10(array, false);
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}
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/**
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* normalizes the real-space probability array.
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*
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* Does not assume anything about the values in the array, beyond that no elements are below 0. It's ok
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* to have values in the array of > 1, or have the sum go above 0.
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*
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* @param array the array to be normalized
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* @return a newly allocated array corresponding the normalized values in array
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*/
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@Requires("array != null")
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@Ensures({"result != null"})
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public static double[] normalizeFromRealSpace(final double[] array) {
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if ( array.length == 0 )
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return array;
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final double sum = sum(array);
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final double[] normalized = new double[array.length];
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if ( sum < 0.0 || sum > 1.0 ) throw new IllegalArgumentException("Values in probability array sum to a negative number " + sum);
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for ( int i = 0; i < array.length; i++ ) {
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normalized[i] = array[i] / sum;
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}
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return normalized;
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}
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public static int maxElementIndex(final double[] array) {
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return maxElementIndex(array, array.length);
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}
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@ -0,0 +1,127 @@
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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.sting.utils.activeregion;
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import com.google.java.contract.Ensures;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.MathUtils;
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import java.util.Collection;
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import java.util.LinkedList;
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/**
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* A band pass filtering version of the activity profile
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*
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* Applies a band pass filter with a Gaussian kernel to the input state probabilities to smooth
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* them out of an interval
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*
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* @author Mark DePristo
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* @since 2011
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*/
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public class BandPassIncrementalActivityProfile extends IncrementalActivityProfile {
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public static final int DEFAULT_FILTER_SIZE = 80;
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private final int filterSize;
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private final double[] GaussianKernel;
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/**
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* Create a band pass activity profile with the default band size
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* @param parser our genome loc parser
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*/
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public BandPassIncrementalActivityProfile(final GenomeLocParser parser) {
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this(parser, DEFAULT_FILTER_SIZE);
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}
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/**
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* Create an activity profile that implements a band pass filter on the states
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* @param parser our genome loc parser
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* @param filterSize the size (in bp) of the band pass filter. The filter size is the number of bp to each
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* side that are included in the band. So a filter size of 1 implies that the actual band
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* is 3 bp, 1 for the center site and 1 on each size. 2 => 5, etc.
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*/
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public BandPassIncrementalActivityProfile(final GenomeLocParser parser, final int filterSize) {
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super(parser);
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if ( filterSize < 0 ) throw new IllegalArgumentException("Filter size must be greater than or equal to 0 but got " + filterSize);
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// setup the Gaussian kernel for the band pass filter
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this.filterSize = filterSize;
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final double[] kernel = new double[getBandSize()];
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for( int iii = 0; iii < 2* filterSize + 1; iii++ ) {
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kernel[iii] = MathUtils.NormalDistribution(filterSize, 55.0, iii);
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}
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this.GaussianKernel = MathUtils.normalizeFromRealSpace(kernel);
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}
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/**
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* Get the size (in bp) of the band pass filter
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* @return a positive integer
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*/
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@Ensures("result >= 1")
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public int getBandSize() {
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return 2 * filterSize + 1;
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}
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/**
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* Get the filter size (which is the size of each wing of the band, minus the center point)
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* @return a positive integer
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*/
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@Ensures("result >= 0")
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public int getFilteredSize() {
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return filterSize;
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}
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/**
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* Get the kernel of this band pass filter. Do not modify returned result
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* @return the kernel used in this band pass filter
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*/
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@Ensures({"result != null", "result.length == getBandSize()"})
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protected double[] getKernel() {
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return GaussianKernel;
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}
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/**
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* Band pass the probabilities in the ActivityProfile, producing a new profile that's band pass filtered
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* @return a new double[] that's the band-pass filtered version of this profile
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*/
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@Override
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protected Collection<ActivityProfileState> processState(final ActivityProfileState justAddedState) {
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final Collection<ActivityProfileState> states = new LinkedList<ActivityProfileState>();
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for ( final ActivityProfileState superState : super.processState(justAddedState) ) {
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for( int jjj = -filterSize; jjj <= filterSize; jjj++ ) {
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final GenomeLoc loc = getLocForOffset(justAddedState.getLoc(), jjj);
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if ( loc != null ) {
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final double newProb = superState.isActiveProb * GaussianKernel[jjj + filterSize];
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states.add(new ActivityProfileState(loc, newProb));
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}
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}
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}
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return states;
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}
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}
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@ -51,35 +51,13 @@ public class IncrementalActivityProfile {
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/**
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* Create a new empty IncrementalActivityProfile
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* @param parser the parser we can use to create genome locs
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* @param parser the parser we can use to create genome locs, cannot be null
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*/
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public IncrementalActivityProfile(final GenomeLocParser parser) {
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this(parser, new ArrayList<ActivityProfileState>(), null);
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}
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if ( parser == null ) throw new IllegalArgumentException("parser cannot be null");
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/**
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* Create a new IncrementalActivityProfile using state list (not copied) and starting at regionStartLoc
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* @param parser the parser we can use to create genome locs
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*/
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@Deprecated
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protected IncrementalActivityProfile(final GenomeLocParser parser, final List<ActivityProfileState> stateList, final GenomeLoc regionStartLoc) {
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this.parser = parser;
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this.stateList = stateList;
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this.regionStartLoc = regionStartLoc;
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}
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/**
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* Create a profile of the same class as this object containing just the provided stateList
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*
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* Used by clients to create derived activity profiles (such as ones without the starting X
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* sites because they've been removed in an ActiveRegion) of the same class.
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*
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* @param isActiveList the active results list to use in the derived instance
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* @return a freshly allocated data set
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*/
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@Deprecated
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protected IncrementalActivityProfile createDerivedProfile(final List<ActivityProfileState> isActiveList) {
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return new IncrementalActivityProfile(parser, isActiveList, regionStartLoc);
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this.stateList = new ArrayList<ActivityProfileState>();
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}
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@Override
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@ -150,6 +128,19 @@ public class IncrementalActivityProfile {
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return stateList;
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}
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/**
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* Get the probabilities of the states as a single linear array of doubles
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* @return a non-null array
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*/
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@Ensures("result != null")
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protected double[] getProbabilitiesAsArray() {
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final double[] probs = new double[getStateList().size()];
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int i = 0;
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for ( final ActivityProfileState state : getStateList() )
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probs[i++] = state.isActiveProb;
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return probs;
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}
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/**
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* Helper function that gets the genome loc for a site offset from relativeLoc, protecting ourselves from
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* falling off the edge of the contig.
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@ -0,0 +1,167 @@
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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.sting.utils.activeregion;
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// the imports for unit testing.
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import net.sf.picard.reference.ReferenceSequenceFile;
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import org.apache.commons.lang.ArrayUtils;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
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import org.testng.Assert;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.util.*;
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public class BandPassIncrementalActivityProfileUnitTest extends BaseTest {
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private GenomeLocParser genomeLocParser;
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@BeforeClass
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public void init() throws FileNotFoundException {
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// sequence
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ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
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genomeLocParser = new GenomeLocParser(seq);
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}
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@DataProvider(name = "BandPassBasicTest")
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public Object[][] makeBandPassTest() {
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final List<Object[]> tests = new LinkedList<Object[]>();
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for ( int start : Arrays.asList(1, 10, 100, 1000) ) {
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for ( boolean precedingIsActive : Arrays.asList(true, false) ) {
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for ( int precedingSites: Arrays.asList(0, 1, 10, 100) ) {
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for ( int bandPassSize : Arrays.asList(0, 1, 10, 100) ) {
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// for ( int start : Arrays.asList(10) ) {
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// for ( boolean precedingIsActive : Arrays.asList(false) ) {
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// for ( int precedingSites: Arrays.asList(0) ) {
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// for ( int bandPassSize : Arrays.asList(1) ) {
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tests.add(new Object[]{ start, precedingIsActive, precedingSites, bandPassSize });
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}
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}
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}
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}
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return tests.toArray(new Object[][]{});
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}
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@Test(dataProvider = "BandPassBasicTest")
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public void testBandPass(final int start, final boolean precedingIsActive, final int nPrecedingSites, final int bandPassSize) {
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final BandPassIncrementalActivityProfile profile = new BandPassIncrementalActivityProfile(genomeLocParser, bandPassSize);
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final int expectedBandSize = bandPassSize * 2 + 1;
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Assert.assertEquals(profile.getBandSize(), expectedBandSize, "Wrong expected band size");
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final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName();
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final double precedingProb = precedingIsActive ? 1.0 : 0.0;
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for ( int i = 0; i < nPrecedingSites; i++ ) {
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final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, i + start);
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final ActivityProfileState state = new ActivityProfileState(loc, precedingProb);
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profile.add(state);
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}
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final GenomeLoc nextLoc = genomeLocParser.createGenomeLoc(contig, nPrecedingSites + start);
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profile.add(new ActivityProfileState(nextLoc, 1.0));
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if ( precedingIsActive == false && nPrecedingSites >= bandPassSize && bandPassSize < start ) {
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// we have enough space that all probs fall on the genome
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final double[] probs = profile.getProbabilitiesAsArray();
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Assert.assertEquals(MathUtils.sum(probs), 1.0 * (nPrecedingSites * precedingProb + 1), 1e-3, "Activity profile doesn't sum to number of non-zero prob states");
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}
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}
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private double[] bandPassInOnePass(final BandPassIncrementalActivityProfile profile, final double[] activeProbArray) {
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final double[] bandPassProbArray = new double[activeProbArray.length];
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// apply the band pass filter for activeProbArray into filteredProbArray
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final double[] GaussianKernel = profile.getKernel();
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for( int iii = 0; iii < activeProbArray.length; iii++ ) {
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final double[] kernel = ArrayUtils.subarray(GaussianKernel, Math.max(profile.getFilteredSize() - iii, 0), Math.min(GaussianKernel.length, profile.getFilteredSize() + activeProbArray.length - iii));
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final double[] activeProbSubArray = ArrayUtils.subarray(activeProbArray, Math.max(0,iii - profile.getFilteredSize()), Math.min(activeProbArray.length,iii + profile.getFilteredSize() + 1));
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bandPassProbArray[iii] = MathUtils.dotProduct(activeProbSubArray, kernel);
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}
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return bandPassProbArray;
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}
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@DataProvider(name = "BandPassComposition")
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public Object[][] makeBandPassComposition() {
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final List<Object[]> tests = new LinkedList<Object[]>();
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for ( int bandPassSize : Arrays.asList(0, 1, 10, 100, BandPassIncrementalActivityProfile.DEFAULT_FILTER_SIZE) ) {
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for ( int integrationLength : Arrays.asList(1, 10, 100, 1000) ) {
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tests.add(new Object[]{ bandPassSize, integrationLength });
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}
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}
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return tests.toArray(new Object[][]{});
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}
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@Test( dataProvider = "BandPassComposition")
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public void testBandPassComposition(final int bandPassSize, final int integrationLength) {
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final int start = 1;
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final BandPassIncrementalActivityProfile profile = new BandPassIncrementalActivityProfile(genomeLocParser, bandPassSize);
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final double[] rawActiveProbs = new double[integrationLength + bandPassSize * 2];
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// add a buffer so that we can get all of the band pass values
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final String contig = genomeLocParser.getContigs().getSequences().get(0).getSequenceName();
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int pos = start;
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int rawProbsOffset = 0;
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for ( int i = 0; i < bandPassSize; i++ ) {
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final GenomeLoc loc = genomeLocParser.createGenomeLoc(contig, pos++);
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final ActivityProfileState state = new ActivityProfileState(loc, 0.0);
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profile.add(state);
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rawActiveProbs[rawProbsOffset++] = 0.0;
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rawActiveProbs[rawActiveProbs.length - rawProbsOffset] = 0.0;
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}
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for ( int i = 0; i < integrationLength; i++ ) {
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final GenomeLoc nextLoc = genomeLocParser.createGenomeLoc(contig, pos++);
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profile.add(new ActivityProfileState(nextLoc, 1.0));
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rawActiveProbs[rawProbsOffset++] = 1.0;
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for ( int j = 0; j < profile.size(); j++ ) {
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Assert.assertTrue(profile.getStateList().get(j).isActiveProb >= 0.0, "State probability < 0 at " + j);
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Assert.assertTrue(profile.getStateList().get(j).isActiveProb <= 1.0 + 1e-3, "State probability > 1 at " + j);
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}
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}
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final double[] expectedProbs = bandPassInOnePass(profile, rawActiveProbs);
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for ( int j = 0; j < profile.size(); j++ ) {
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Assert.assertEquals(profile.getStateList().get(j).isActiveProb, expectedProbs[j], "State probability not expected at " + j);
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}
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}
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}
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@ -85,7 +85,9 @@ public class IncrementalActivityProfileUnitTest extends BaseTest {
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public IncrementalActivityProfile makeProfile() {
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switch ( type ) {
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case Base: return new IncrementalActivityProfile(genomeLocParser);
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case BandPass: //return new BandPassActivityProfile(genomeLocParser);
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case BandPass:
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// zero size => equivalent to IncrementalActivityProfile
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return new BandPassIncrementalActivityProfile(genomeLocParser, 0);
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default: throw new IllegalStateException(type.toString());
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}
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}
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@ -111,13 +113,11 @@ public class IncrementalActivityProfileUnitTest extends BaseTest {
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@DataProvider(name = "BasicActivityProfileTestProvider")
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public Object[][] makeQualIntervalTestProvider() {
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for ( final ProfileType type : ProfileType.values() ) {
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if ( type != ProfileType.BandPass ) { // todo -- re-enable
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new BasicActivityProfileTestProvider(type, Arrays.asList(1.0), true, 0, 1);
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new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 0.0), true, 0, 1, 2);
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new BasicActivityProfileTestProvider(type, Arrays.asList(0.0, 1.0), false, 0, 1, 2);
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new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 0.0, 1.0), true, 0, 1, 2, 3);
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new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 1.0, 1.0), true, 0, 3);
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}
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new BasicActivityProfileTestProvider(type, Arrays.asList(1.0), true, 0, 1);
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new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 0.0), true, 0, 1, 2);
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new BasicActivityProfileTestProvider(type, Arrays.asList(0.0, 1.0), false, 0, 1, 2);
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new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 0.0, 1.0), true, 0, 1, 2, 3);
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new BasicActivityProfileTestProvider(type, Arrays.asList(1.0, 1.0, 1.0), true, 0, 3);
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}
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return BasicActivityProfileTestProvider.getTests(BasicActivityProfileTestProvider.class);
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@ -135,20 +135,15 @@ public class IncrementalActivityProfileUnitTest extends BaseTest {
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double p = cfg.probs.get(i);
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GenomeLoc loc = genomeLocParser.createGenomeLoc(cfg.regionStart.getContig(), cfg.regionStart.getStart() + i, cfg.regionStart.getStart() + i);
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profile.add(new ActivityProfileState(loc, p));
|
||||
Assert.assertFalse(profile.isEmpty());
|
||||
Assert.assertFalse(profile.isEmpty(), "Profile shouldn't be empty after adding a state");
|
||||
}
|
||||
Assert.assertEquals(profile.regionStartLoc, genomeLocParser.createGenomeLoc(cfg.regionStart.getContig(), cfg.regionStart.getStart(), cfg.regionStart.getStart() ));
|
||||
Assert.assertEquals(profile.regionStartLoc, genomeLocParser.createGenomeLoc(cfg.regionStart.getContig(), cfg.regionStart.getStart(), cfg.regionStart.getStart() ), "Start loc should be the start of the region");
|
||||
|
||||
Assert.assertEquals(profile.size(), cfg.probs.size());
|
||||
Assert.assertEquals(profile.size(), cfg.probs.size(), "Should have exactly the number of states we expected to add");
|
||||
assertProbsAreEqual(profile.stateList, cfg.probs);
|
||||
|
||||
// TODO -- reanble tests
|
||||
//assertRegionsAreEqual(profile.createActiveRegions(0, 100), cfg.expectedRegions);
|
||||
|
||||
Assert.assertEquals(profile.createDerivedProfile(profile.stateList).getClass(), profile.getClass());
|
||||
|
||||
final List<ActivityProfileState> empty = new LinkedList<ActivityProfileState>();
|
||||
Assert.assertEquals(profile.createDerivedProfile(empty).size(), 0);
|
||||
}
|
||||
|
||||
private void assertRegionsAreEqual(List<ActiveRegion> actual, List<ActiveRegion> expected) {
|
||||
|
|
|
|||
Loading…
Reference in New Issue