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Update to AminoAcidTransition eval module 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3783 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-07-13 17:12:03 +00:00
parent 9cc1a411b2
commit 9d2a485532
2 changed files with 37 additions and 10 deletions
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13
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -179,6 +179,15 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
Set<String> rsIDsToExclude = null;
@Argument(shortName="aatk", fullName="aminoAcidTransitionKey", doc="required for the amino acid transition table; this is the key in the info field for the VCF for the transition", required = false)
protected String aminoAcidTransitionKey = null;
@Argument(shortName="aats", fullName="aminoAcidTransitionSplit", doc="required for the amino acid transition table, this is the key on which to split the info field value to get the reference and alternate amino acids", required=false)
protected String aminoAcidTransitionSplit = null;
@Argument(shortName="aatUseCodons", fullName="aminoAcidsRepresentedByCodons", doc="for the amino acid table, specifiy that the transitions are represented as codon changes, and not directly amino acid names", required = false)
protected boolean aatUseCodons = false;
// --------------------------------------------------------------------------------------------------------------
//
// private walker data
@ -428,9 +437,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
} catch (NoSuchMethodException e) {
throw new StingException(String.format("Cannot find expected constructor for class '%s': must have constructor accepting a single VariantEval2Walker object", c.getSimpleName()));
} catch (IllegalAccessException e) {
throw new StingException(String.format("Cannot instantiate class '%s':", c.getSimpleName()));
throw new StingException(String.format("Cannot instantiate class '%s' (Illegal Access):", c.getSimpleName()));
} catch (InvocationTargetException e) {
throw new StingException(String.format("Cannot instantiate class '%s':", c.getSimpleName()));
throw new StingException(String.format("Cannot instantiate class '%s' (Invocation): %s", c.getSimpleName(), e.getMessage()));
}
}

34
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java
View File

@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
@ -71,11 +72,11 @@ public class AminoAcidTransition extends VariantEvaluator {
}
public double getRatio() {
return ( (double) ti )/tv;
return ( (double) ti )/(1.0+tv);
}
public String toString() {
return String.format("%d:%d:%d:%f",getTotal(),ti,tv,getRatio());
return String.format("%d:%d:%d:%.2f",getTotal(),ti,tv,getRatio());
}
}
@ -132,13 +133,22 @@ public class AminoAcidTransition extends VariantEvaluator {
super(parent);
getParsingInformation(parent);
lookup = new AminoAcidTable();
acidTable = new AminoAcidTiTvTable();
}
private void getParsingInformation(VariantEvalWalker parent) {
// todo -- allow me to be flexible
infoKey = "something";
infoValueSplit = "somethingElse";
useCodons = false;
if ( enabled() ) {
infoKey = parent.aminoAcidTransitionKey;
infoValueSplit = parent.aminoAcidTransitionSplit;
useCodons = parent.aatUseCodons;
if ( infoKey == null ) {
throw new StingException("No info-field key provided for amino acid tabulation. Please provide the appropriate key with -aatk.");
}
if ( infoValueSplit == null ) {
throw new StingException("No split string provided for amino acid tabulation. Please provide the split string with -aats");
}
}
}
public String getName() {
@ -161,8 +171,14 @@ public class AminoAcidTransition extends VariantEvaluator {
String interesting = null;
if ( eval != null && eval.hasAttribute(infoKey) ) {
String[] parsedNames = ( (String) eval.getAttribute(infoKey)).split(infoValueSplit);
String first = parsedNames [0];
String second = parsedNames [1];
String first = "none";
String second = "none";
try {
first = parsedNames [0];
second = parsedNames [1];
} catch (ArrayIndexOutOfBoundsException e) {
veWalker.getLogger().warn("Error prasing variant context with value "+eval.getAttribute(infoKey));
}
AminoAcid reference;
AminoAcid alternate;
if ( useCodons ) {
@ -173,6 +189,8 @@ public class AminoAcidTransition extends VariantEvaluator {
alternate = lookup.getAminoAcidByCode(second);
}
//veWalker.getLogger().info(String.format("%s\t%s\t%s\t%s",first,second,reference,alternate));
if ( reference == null ) {
interesting = "Unknown Reference Codon";
} else if ( alternate == null ) {