Fixes to support evaluations with TableType elements - each such object now gets a separate entry in the output table. Added codon degeneracy stratification. Handle null elements in reports (useful for debugging).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5101 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
a264b16358
commit
58f0ecff89
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@ -66,10 +66,12 @@ public class GATKReportColumn extends TreeMap<Object, Object> {
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int maxWidth = columnName.length();
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for (Object obj : this.values()) {
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int width = obj.toString().length();
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if (obj != null) {
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int width = obj.toString().length();
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if (width > maxWidth) {
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maxWidth = width;
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if (width > maxWidth) {
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maxWidth = width;
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}
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}
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}
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@ -108,7 +108,7 @@ public class GATKReportTable {
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* @return true if the name is valid, false if otherwise
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*/
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private boolean isValidName(String name) {
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Pattern p = Pattern.compile("[^a-zA-Z0-9_]");
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Pattern p = Pattern.compile("[^a-zA-Z0-9_\\-\\.]");
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Matcher m = p.matcher(name);
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return !m.find();
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@ -546,7 +546,7 @@ public class GATKReportTable {
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Object obj = columns.get(columnName).getWithoutSideEffects(primaryKey);
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if (needsPadding) { out.printf(" "); }
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out.printf(columnWidths.get(columnName), obj.toString());
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out.printf(columnWidths.get(columnName), obj == null ? "null" : obj.toString());
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needsPadding = true;
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}
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@ -17,6 +17,8 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.TreeReducible;
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import org.broadinstitute.sting.gatk.walkers.Window;
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import org.broadinstitute.sting.gatk.walkers.variantrecalibration.Tranche;
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import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators.StandardEval;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.evaluators.VariantEvaluator;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.RequiredStratification;
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@ -30,12 +32,12 @@ import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.util.Stat
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.StingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.report.utils.TableType;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import java.io.File;
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import java.io.PrintStream;
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import java.lang.reflect.Field;
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import java.util.*;
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@ -84,6 +86,15 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
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@Argument(fullName="minPhaseQuality", shortName="mpq", doc="Minimum phasing quality", required=false)
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protected double MIN_PHASE_QUALITY = 10.0;
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@Argument(shortName="family", doc="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
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protected String FAMILY_STRUCTURE;
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@Argument(shortName="mvq", fullName="mendelianViolationQualThreshold", doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation", required=false)
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protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50;
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@Argument(fullName="tranchesFile", shortName="tf", doc="The input tranches file describing where to cut the data", required=false)
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private String TRANCHE_FILENAME = null;
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// Variables
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private Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions = new TreeSet<VariantContextUtils.JexlVCMatchExp>();
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private Set<String> compNames = new TreeSet<String>();
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@ -317,14 +328,7 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
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for (Field field : datamap.keySet()) {
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field.setAccessible(true);
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if (field.get(vei) instanceof TableType) {
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TableType t = (TableType) field.get(vei);
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for ( Object o : t.getColumnKeys() ) {
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String c = (String) o;
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table.addColumn(c, 0.0);
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}
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} else {
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if (! (field.get(vei) instanceof TableType) ) {
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table.addColumn(field.getName(), 0.0);
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}
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}
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@ -381,6 +385,16 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
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// Initialize select expressions
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jexlExpressions.addAll(VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS));
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// Add select expressions for anything in the tranches file
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if ( TRANCHE_FILENAME != null ) {
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// we are going to build a few select names automatically from the tranches file
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for ( Tranche t : Tranche.readTraches(new File(TRANCHE_FILENAME)) ) {
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logger.info("Adding select for all variant above the pCut of : " + t);
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SELECT_EXPS.add(String.format(VariantRecalibrator.VQS_LOD_KEY + " >= %.2f", t.minVQSLod));
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SELECT_NAMES.add(String.format("FDR-%.2f", t.fdr));
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}
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}
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// Initialize the set of stratifications and evaluations to use
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stratificationObjects = initializeStratificationObjects(NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
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Set<Class<? extends VariantEvaluator>> evaluationObjects = initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
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@ -617,6 +631,22 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
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return MIN_PHASE_QUALITY;
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}
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/**
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* Return the family structure to be used with the MendelianViolationEvaluator module
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* @return the family structure string
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*/
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public String getFamilyStructure() {
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return FAMILY_STRUCTURE;
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}
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/**
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* Return the mendelian violation qual threshold to be used with the MendelianViolationEvaluator module
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* @return the mendelian violation qual threshold
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*/
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public double getMendelianViolationQualThreshold() {
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return MENDELIAN_VIOLATION_QUAL_THRESHOLD;
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}
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/**
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* Collect relevant information from each variant in the supplied VCFs
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*/
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@ -703,12 +733,10 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
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for ( VariantEvaluator ve : nec.getEvaluationClassList().values() ) {
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ve.finalizeEvaluation();
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GATKReportTable table = report.getTable(ve.getClass().getSimpleName());
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AnalysisModuleScanner scanner = new AnalysisModuleScanner(ve);
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Map<Field, DataPoint> datamap = scanner.getData();
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// handle TableTypes
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for (Field field : datamap.keySet()) {
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try {
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field.setAccessible(true);
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@ -716,6 +744,26 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
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if (field.get(ve) instanceof TableType) {
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TableType t = (TableType) field.get(ve);
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String subTableName = ve.getClass().getSimpleName() + "." + field.getName();
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String subTableDesc = datamap.get(field).description();
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report.addTable(subTableName, subTableDesc);
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GATKReportTable table = report.getTable(subTableName);
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table.addPrimaryKey("entry", false);
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table.addColumn(subTableName, subTableName);
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for ( VariantStratifier vs : stratificationObjects ) {
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String columnName = vs.getClass().getSimpleName();
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table.addColumn(columnName, "unknown");
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}
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for ( Object o : t.getColumnKeys() ) {
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String c = (String) o;
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table.addColumn(c, 0.0);
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}
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for (int row = 0; row < t.getRowKeys().length; row++) {
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String r = (String) t.getRowKeys()[row];
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@ -732,27 +780,19 @@ public class NewVariantEvalWalker extends RodWalker<Integer, Integer> implements
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table.set(newStateKey, c, t.getCell(row, col));
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}
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}
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}
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} catch (IllegalAccessException e) {
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throw new StingException("IllegalAccessException: " + e);
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}
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}
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} else {
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GATKReportTable table = report.getTable(ve.getClass().getSimpleName());
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for ( VariantStratifier vs : stratificationObjects ) {
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String columnName = vs.getClass().getSimpleName();
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for ( VariantStratifier vs : stratificationObjects ) {
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String columnName = vs.getClass().getSimpleName();
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table.set(stateKey.toString(), columnName, stateKey.get(vs.getClass().getSimpleName()));
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}
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table.set(stateKey.toString(), columnName, stateKey.get(vs.getClass().getSimpleName()));
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}
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for (Field field : datamap.keySet()) {
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try {
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field.setAccessible(true);
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if ( !(field.get(ve) instanceof TableType) ) {
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table.set(stateKey.toString(), field.getName(), field.get(ve));
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}
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} catch (IllegalAccessException e) {
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throw new ReviewedStingException("Unable to access a data field in a VariantEval analysis module: " + e);
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throw new StingException("IllegalAccessException: " + e);
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}
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}
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}
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@ -246,7 +246,7 @@ public class GenotypeConcordance extends VariantEvaluator {
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private boolean warnedAboutValidationData = false;
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public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, NewEvaluationContext group) {
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public String update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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String interesting = null;
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// sanity check that we at least have either eval or validation data
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@ -321,7 +321,10 @@ public class GenotypeConcordance extends VariantEvaluator {
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sampleStats.incrValue(sample, truth, called);
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if ( evalAC != null && validationAC != null) {
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alleleCountStats.incrValue(evalAC,truth,called);
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alleleCountStats.incrValue(validationAC,truth,called);
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//System.err.println(evalAC + " " + validationAC);
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//alleleCountStats.incrValue(validationAC,truth,called);
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}
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}
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}
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@ -461,12 +464,18 @@ class SampleStats implements TableType {
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* @return a list of objects, in this case strings, that are the column names
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*/
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public Object[] getColumnKeys() {
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return new String[]{"total_true_ref","%_ref/ref","n_ref/no-call",
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"n_ref/ref","n_ref/het","n_ref/hom",
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"total_true_het","%_het/het","n_het/no-call",
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"n_het/ref","n_het/het","n_het/hom",
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"total_true_hom","%_hom/hom","n_hom/no-call",
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"n_hom/ref","n_hom/het","n_hom/hom"};
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// return new String[]{"total_true_ref","%_ref/ref","n_ref/no-call",
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// "n_ref/ref","n_ref/het","n_ref/hom",
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// "total_true_het","%_het/het","n_het/no-call",
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// "n_het/ref","n_het/het","n_het/hom",
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// "total_true_hom","%_hom/hom","n_hom/no-call",
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// "n_hom/ref","n_hom/het","n_hom/hom"};
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return new String[]{"total_true_ref","pct_ref_vs_ref","n_ref_vs_no-call",
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"n_ref_vs_ref","n_ref_vs_het","n_ref_vs_hom",
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"total_true_het","pct_het_vs_het","n_het_vs_no-call",
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"n_het_vs_ref","n_het_vs_het","n_het_vs_hom",
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"total_true_hom","pct_hom_vs_hom","n_hom_vs_no-call",
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"n_hom_vs_ref","n_hom_vs_het","n_hom_vs_hom"};
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}
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@ -6,6 +6,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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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.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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@ -60,6 +61,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
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long KidHomVar_ParentHomRef;
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TrioStructure trio;
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double mendelianViolationQualThreshold;
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private static Pattern FAMILY_PATTERN = Pattern.compile("(.*)\\+(.*)=(.*)");
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@ -82,25 +84,21 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
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}
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// todo: fix
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public void initialize(NewVariantEvalWalker walker) {
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trio = parseTrioDescription(walker.getFamilyStructure());
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mendelianViolationQualThreshold = walker.getMendelianViolationQualThreshold();
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}
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//public MendelianViolationEvaluator(VariantEvalWalker parent) {
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//super(parent);
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//if (enabled()) {
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//trio = parseTrioDescription(parent.FAMILY_STRUCTURE);
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//parent.getLogger().debug(String.format("Found a family pattern: %s mom=%s dad=%s child=%s",
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//parent.FAMILY_STRUCTURE, trio.mom, trio.dad, trio.child));
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//}
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//}
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public boolean enabled() {
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//return getVEWalker().FAMILY_STRUCTURE != null;
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return false;
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return true;
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}
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private double getQThreshold() {
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//return getVEWalker().MENDELIAN_VIOLATION_QUAL_THRESHOLD / 10; // we aren't 10x scaled in the GATK a la phred
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return 0.0;
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return mendelianViolationQualThreshold / 10; // we aren't 10x scaled in the GATK a la phred
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//return 0.0;
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}
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public String getName() {
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@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.NewVariantEvalWalker;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.Degeneracy;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications.Sample;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.Analysis;
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import org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.tags.DataPoint;
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@ -171,8 +172,19 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval
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@Override
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public boolean stateIsApplicable(StateKey stateKey) {
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String className = Sample.class.getSimpleName();
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String sampleClassName = Sample.class.getSimpleName();
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String degeneracyClassName = Degeneracy.class.getSimpleName();
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return !(stateKey.containsKey(className) && !stateKey.get(className).equalsIgnoreCase("all"));
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//return !(stateKey.containsKey(sampleClassName) && !stateKey.get(sampleClassName).equalsIgnoreCase("all"));
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if (stateKey.containsKey(sampleClassName) && !stateKey.get(sampleClassName).equalsIgnoreCase("all")) {
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return false;
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}
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if (stateKey.containsKey(degeneracyClassName) && !stateKey.get(degeneracyClassName).equalsIgnoreCase("all")) {
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return false;
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}
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return true;
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}
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}
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@ -0,0 +1,98 @@
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package org.broadinstitute.sting.playground.gatk.walkers.newvarianteval.stratifications;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Set;
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public class Degeneracy extends VariantStratifier {
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private ArrayList<String> states;
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private HashMap<String, String> degeneracies;
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@Override
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public void initialize(Set<VariantContextUtils.JexlVCMatchExp> jexlExpressions, Set<String> compNames, Set<String> knownNames, Set<String> evalNames, Set<String> sampleNames) {
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states = new ArrayList<String>();
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states.add("1-fold");
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states.add("2-fold");
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states.add("3-fold");
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states.add("4-fold");
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states.add("6-fold");
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states.add("all");
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degeneracies = new HashMap<String, String>();
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degeneracies.put("Ile", "3-fold");
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degeneracies.put("Leu", "6-fold");
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degeneracies.put("Val", "4-fold");
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degeneracies.put("Phe", "2-fold");
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degeneracies.put("Met", "1-fold");
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degeneracies.put("Cys", "2-fold");
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degeneracies.put("Ala", "4-fold");
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degeneracies.put("Gly", "4-fold");
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degeneracies.put("Pro", "4-fold");
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degeneracies.put("Thr", "4-fold");
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degeneracies.put("Ser", "6-fold");
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degeneracies.put("Tyr", "2-fold");
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degeneracies.put("Try", "1-fold");
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degeneracies.put("Trp", "1-fold");
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degeneracies.put("Gln", "2-fold");
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degeneracies.put("Asn", "2-fold");
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degeneracies.put("His", "2-fold");
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degeneracies.put("Glu", "2-fold");
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degeneracies.put("Asp", "2-fold");
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degeneracies.put("Lys", "2-fold");
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degeneracies.put("Arg", "6-fold");
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degeneracies.put("Stop", "3-fold");
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}
|
||||
|
||||
public ArrayList<String> getAllStates() {
|
||||
return states;
|
||||
}
|
||||
|
||||
public ArrayList<String> getRelevantStates(ReferenceContext ref, VariantContext comp, String compName, VariantContext eval, String sampleName) {
|
||||
ArrayList<String> relevantStates = new ArrayList<String>();
|
||||
|
||||
relevantStates.add("all");
|
||||
|
||||
if (eval != null && eval.isVariant()) {
|
||||
String type = null;
|
||||
String aa = null;
|
||||
|
||||
if (eval.getAttributeAsString("refseq.functionalClass") != null) {
|
||||
type = eval.getAttributeAsString("refseq.functionalClass");
|
||||
aa = eval.getAttributeAsString("refseq.variantAA");
|
||||
} else if (eval.getAttributeAsString("refseq.functionalClass_1") != null) {
|
||||
int annotationId = 1;
|
||||
String key;
|
||||
|
||||
do {
|
||||
key = String.format("refseq.functionalClass_%d", annotationId);
|
||||
|
||||
String newtype = eval.getAttributeAsString(key);
|
||||
|
||||
if ( newtype != null &&
|
||||
( type == null ||
|
||||
( type.equals("silent") && !newtype.equals("silent") ) ||
|
||||
( type.equals("missense") && newtype.equals("nonsense") ) )
|
||||
) {
|
||||
type = newtype;
|
||||
|
||||
String aakey = String.format("refseq.variantAA_%d", annotationId);
|
||||
aa = eval.getAttributeAsString(aakey);
|
||||
}
|
||||
|
||||
annotationId++;
|
||||
} while (eval.getAttributeAsString(key) != null);
|
||||
}
|
||||
|
||||
if (aa != null && degeneracies.containsKey(aa)) {
|
||||
relevantStates.add(degeneracies.get(aa));
|
||||
}
|
||||
}
|
||||
|
||||
return relevantStates;
|
||||
}
|
||||
}
|
||||
|
|
@ -52,29 +52,31 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
|
|||
|
||||
public void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) {
|
||||
for ( VariantEvaluator evaluation : evaluationInstances.values() ) {
|
||||
// we always call update0 in case the evaluation tracks things like number of bases covered
|
||||
//evaluation.update0(tracker, ref, context);
|
||||
synchronized ( evaluation ) {
|
||||
// we always call update0 in case the evaluation tracks things like number of bases covered
|
||||
//evaluation.update0(tracker, ref, context);
|
||||
|
||||
// the other updateN methods don't see a null context
|
||||
if ( tracker == null )
|
||||
continue;
|
||||
// the other updateN methods don't see a null context
|
||||
if ( tracker == null )
|
||||
continue;
|
||||
|
||||
// now call the single or paired update function
|
||||
switch ( evaluation.getComparisonOrder() ) {
|
||||
case 1:
|
||||
if (eval != null) {
|
||||
evaluation.update1(eval, tracker, ref, context);
|
||||
}
|
||||
// now call the single or paired update function
|
||||
switch ( evaluation.getComparisonOrder() ) {
|
||||
case 1:
|
||||
if (eval != null) {
|
||||
evaluation.update1(eval, tracker, ref, context);
|
||||
}
|
||||
|
||||
break;
|
||||
case 2:
|
||||
if (eval != null) {
|
||||
evaluation.update2(eval, comp, tracker, ref, context);
|
||||
}
|
||||
break;
|
||||
case 2:
|
||||
if (eval != null) {
|
||||
evaluation.update2(eval, comp, tracker, ref, context);
|
||||
}
|
||||
|
||||
break;
|
||||
default:
|
||||
throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation);
|
||||
break;
|
||||
default:
|
||||
throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue