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Support for reading in table of rsIDs -> dbSNP builds to back generate a dbSNP build X from a single file. Very useful indeed. dbSNP -> VC now captures the rsID in the context 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2837 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-02-12 22:40:55 +00:00
parent 28f24ca2ae
commit a1a3d5fcb0
4 changed files with 65 additions and 6 deletions
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2
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContext.java
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@ -215,7 +215,7 @@ public class VariantContext {
* @param attributes
*/
public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
this(name, loc, alleles, genotypeCollectionToMap(new HashMap<String, Genotype>(), genotypes), negLog10PError, filters, attributes);
this(name, loc, alleles, genotypes != null ? genotypeCollectionToMap(new HashMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes);
}
/**

5
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -93,7 +93,10 @@ public class VariantContextAdaptors {
alleles.add(new Allele(alt, false));
}
VariantContext vc = new VariantContext(name, dbsnp.getLocation(), alleles);
Map<String, String> attributes = new HashMap<String, String>();
attributes.put("ID", dbsnp.getRS_ID());
Collection<Genotype> genotypes = null;
VariantContext vc = new VariantContext(name, dbsnp.getLocation(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes);
vc.validate();
return vc;
} else

3
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java
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@ -100,6 +100,9 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
Genotype dadG = vc.getGenotype(trio.dad);
Genotype childG = vc.getGenotype(trio.child);
if ( momG == null || dadG == null || childG == null )
throw new IllegalArgumentException(String.format("VariantContext didn't contain genotypes for expected trio members: mom=%s dad=%s child=%s", trio.mom, trio.dad, trio.child));
if ( includeGenotype(momG) && includeGenotype(dadG) && includeGenotype(childG) ) {
// all genotypes are good, so let's see if child is a violation

61
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
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@ -17,6 +17,7 @@ import java.util.*;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.io.File;
import java.io.FileNotFoundException;
// todo -- evalations should support comment lines
// todo -- add Mendelian variable explanations (nDeNovo and nMissingTransmissions)
@ -120,6 +121,14 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
/** Right now we will only be looking at SNPS */
EnumSet<VariantContext.Type> ALLOW_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP);
@Argument(shortName="rsID", fullName="rsID", doc="If provided, list of rsID and build number for capping known snps by their build date", required=false)
protected String rsIDFile = null;
@Argument(shortName="maxRsIDBuild", fullName="maxRsIDBuild", doc="If provided, only variants with rsIDs <= maxRsIDBuild will be included in the set of knwon snps", required=false)
protected int maxRsIDBuild = Integer.MAX_VALUE;
Set<String> rsIDsToExclude = null;
// --------------------------------------------------------------------------------------------------------------
//
// private walker data
@ -218,8 +227,50 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
if ( outputVCF != null )
writer = new VCFWriter(new File(outputVCF));
if ( rsIDFile != null ) {
if ( maxRsIDBuild == Integer.MAX_VALUE )
throw new IllegalArgumentException("rsIDFile " + rsIDFile + " was given but associated max RSID build parameter wasn't available");
rsIDsToExclude = getrsIDsToExclude(new File(rsIDFile), maxRsIDBuild);
}
}
private static Set<String> getrsIDsToExclude(File rsIDFile, int maxRsIDBuild) {
List<String> toExclude = new LinkedList<String>();
int n = 1;
try {
for ( String line : new xReadLines(rsIDFile) ) {
String parts[] = line.split(" ");
if ( parts.length != 2 )
throw new StingException("Invalid rsID / build pair at " + n + " line = " + line );
//System.out.printf("line %s %s %s%n", line, parts[0], parts[1]);
if ( Integer.valueOf(parts[1]) > maxRsIDBuild ) {
//System.out.printf("Excluding %s%n", line);
toExclude.add("rs"+parts[0]);
}
n++;
if ( n % 1000000 == 0 )
logger.info(String.format("Read %d rsIDs from rsID -> build file", n));
}
} catch (FileNotFoundException e) {
throw new StingException(e.getMessage());
}
logger.info(String.format("Excluding %d of %d (%.2f%%) rsIDs found from builds > %d",
toExclude.size(), n, ((100.0 * toExclude.size())/n), maxRsIDBuild));
return new HashSet<String>(toExclude);
}
private final static String ID = "ID";
private boolean excludeComp(VariantContext vc) {
String id = vc != null && vc.hasAttribute(ID) ? vc.getAttributeAsString(ID) : null;
boolean ex = rsIDsToExclude != null && id != null && rsIDsToExclude.contains(id);
//System.out.printf("Testing id %s ex=%b against %s%n", id, ex, vc);
return ex;
}
private void determineAllEvalations() {
evaluationClasses = PackageUtils.getClassesImplementingInterface(VariantEvaluator.class);
@ -426,18 +477,20 @@ public class VariantEval2Walker extends RodWalker<Integer, Integer> {
// todo -- we need to deal with dbSNP where there can be multiple records at the same start site. A potential solution is to
// todo -- allow the variant evaluation to specify the type of variants it wants to see and only take the first such record at a site
Map<String, VariantContext> bindings = new HashMap<String, VariantContext>();
bindVariantContexts(bindings, evalNames, tracker, context);
bindVariantContexts(bindings, compNames, tracker, context);
bindVariantContexts(bindings, evalNames, tracker, context, false);
bindVariantContexts(bindings, compNames, tracker, context, true);
return bindings;
}
private void bindVariantContexts(Map<String, VariantContext> map, Collection<String> names,
RefMetaDataTracker tracker, AlignmentContext context ) {
RefMetaDataTracker tracker, AlignmentContext context, boolean allowExcludes ) {
for ( String name : names ) {
Collection<VariantContext> contexts = tracker.getVariantContexts(name, ALLOW_VARIANT_CONTEXT_TYPES, context.getLocation(), true, true);
if ( context.size() > 1 )
throw new StingException("Found multiple variant contexts at " + context.getLocation());
map.put(name, contexts.size() == 1 ? contexts.iterator().next() : null);
VariantContext vc = contexts.size() == 1 ? contexts.iterator().next() : null;
map.put(name, allowExcludes && excludeComp(vc) ? null : vc);
}
}