zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Renaming quantitative trait to OtherPhenotype which is now a String not a double 

-- we can now use PED file to represent population data or other arbitrary phenotype data, not just doubles
This commit is contained in:
Mark DePristo 2011-10-05 12:26:33 -07:00
parent 51ecc20867
commit e7c80f7c45
6 changed files with 43 additions and 53 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/java/src/org/broadinstitute/sting/gatk/samples/Affection.java
View File

@ -28,8 +28,8 @@ package org.broadinstitute.sting.gatk.samples;
* Categorical sample trait for association and analysis
*
* Samples can have unknown status, be affected or unaffected by the
* categorical trait, or they can be marked as actually having a
* quantitative trait value (stored in an associated value in the Sample class)
* categorical trait, or they can be marked as actually having an
* other trait value (stored in an associated value in the Sample class)
*
* @author Mark DePristo
* @since Sept. 2011
@ -41,6 +41,6 @@ public enum Affection {
AFFECTED,
/** Unaffected by the disease */
UNAFFECTED,
/** A quantitative trait: value of the trait is stored elsewhere */
QUANTITATIVE
/** An "other" trait: value of the trait is stored elsewhere and is an arbitrary string */
OTHER
}

10
public/java/src/org/broadinstitute/sting/gatk/samples/PedReader.java
View File

@ -63,6 +63,8 @@ import java.util.*;
* A PED file must have 1 and only 1 phenotype in the sixth column. The phenotype can be either a
* quantitative trait or an affection status column: PLINK will automatically detect which type
* (i.e. based on whether a value other than 0, 1, 2 or the missing genotype code is observed).
* Note that the GATK actually supports arbitrary values for quantitative trait -- not just doubles --
* and are actually representing these values as strings instead of doubles
*
* NOTE Quantitative traits with decimal points must be coded with a period/full-stop character and
* not a comma, i.e. 2.394 not 2,394
@ -212,7 +214,7 @@ public class PedReader {
splits.add(parts);
lineNo++;
}
logger.info("Trait is quantitative? " + isQT);
logger.info("Phenotype is other? " + isQT);
// now go through and parse each record
lineNo = 1;
@ -220,7 +222,7 @@ public class PedReader {
for ( final String[] parts : splits ) {
String familyID = null, individualID, paternalID = null, maternalID = null;
Gender sex = Gender.UNKNOWN;
double quantitativePhenotype = Sample.UNSET_QT;
String quantitativePhenotype = Sample.UNSET_QT;
Affection affection = Affection.UNKNOWN;
if ( familyPos != -1 ) familyID = maybeMissing(parts[familyPos]);
@ -239,8 +241,8 @@ public class PedReader {
if ( parts[phenotypePos].equals(MISSING_VALUE1) )
affection = Affection.UNKNOWN;
else {
affection = Affection.QUANTITATIVE;
quantitativePhenotype = Double.valueOf(parts[phenotypePos]);
affection = Affection.OTHER;
quantitativePhenotype = parts[phenotypePos];
}
} else {
if ( parts[phenotypePos].equals(MISSING_VALUE1) ) affection = Affection.UNKNOWN;

30
public/java/src/org/broadinstitute/sting/gatk/samples/Sample.java
View File

@ -12,22 +12,22 @@ import java.util.Map;
public class Sample implements Comparable<Sample> { // implements java.io.Serializable {
final private String familyID, paternalID, maternalID;
final private Gender gender;
final private double quantitativePhenotype;
final private String otherPhenotype;
final private Affection affection;
final private String ID;
final private SampleDB infoDB;
final private Map<String, Object> properties = new HashMap<String, Object>();
public final static double UNSET_QT = Double.NaN;
public final static String UNSET_QT = null;
public Sample(final String ID, final SampleDB infoDB,
final String familyID, final String paternalID, final String maternalID,
final Gender gender, final Affection affection, final double quantitativePhenotype) {
final Gender gender, final Affection affection, final String otherPhenotype) {
this.familyID = familyID;
this.paternalID = paternalID;
this.maternalID = maternalID;
this.gender = gender;
this.quantitativePhenotype = quantitativePhenotype;
this.otherPhenotype = otherPhenotype;
this.affection = affection;
this.ID = ID;
this.infoDB = infoDB;
@ -35,8 +35,8 @@ public class Sample implements Comparable<Sample> { // implements java.io.Serial
protected Sample(final String ID,
final String familyID, final String paternalID, final String maternalID,
final Gender gender, final Affection affection, final double quantitativePhenotype) {
this(ID, null, familyID, paternalID, maternalID, gender, affection, quantitativePhenotype);
final Gender gender, final Affection affection, final String otherPhenotype) {
this(ID, null, familyID, paternalID, maternalID, gender, affection, otherPhenotype);
}
protected Sample(final String ID,
@ -51,8 +51,8 @@ public class Sample implements Comparable<Sample> { // implements java.io.Serial
this(ID, infoDB, familyID, paternalID, maternalID, gender, Affection.UNKNOWN, UNSET_QT);
}
public Sample(final String ID, final SampleDB infoDB, final Affection affection, final double quantitativePhenotype) {
this(ID, infoDB, null, null, null, Gender.UNKNOWN, affection, quantitativePhenotype);
public Sample(final String ID, final SampleDB infoDB, final Affection affection, final String otherPhenotype) {
this(ID, infoDB, null, null, null, Gender.UNKNOWN, affection, otherPhenotype);
}
public Sample(String id, SampleDB infoDB) {
@ -86,12 +86,12 @@ public class Sample implements Comparable<Sample> { // implements java.io.Serial
return affection;
}
public boolean hasQuantitativeTrait() {
return affection == Affection.QUANTITATIVE;
public boolean hasOtherPhenotype() {
return affection == Affection.OTHER;
}
public double getQuantitativePhenotype() {
return quantitativePhenotype;
public String getOtherPhenotype() {
return otherPhenotype;
}
/**
@ -127,7 +127,7 @@ public class Sample implements Comparable<Sample> { // implements java.io.Serial
public String toString() {
return String.format("Sample %s fam=%s dad=%s mom=%s gender=%s affection=%s qt=%s props=%s",
getID(), getFamilyID(), getPaternalID(), getMaternalID(), getGender(), getAffection(),
getQuantitativePhenotype(), properties);
getOtherPhenotype(), properties);
}
// // -------------------------------------------------------------------------------------
@ -174,7 +174,7 @@ public class Sample implements Comparable<Sample> { // implements java.io.Serial
equalOrNull(paternalID, otherSample.paternalID) &&
equalOrNull(maternalID, otherSample.maternalID) &&
equalOrNull(gender, otherSample.gender) &&
equalOrNull(quantitativePhenotype, otherSample.quantitativePhenotype) &&
equalOrNull(otherPhenotype, otherSample.otherPhenotype) &&
equalOrNull(affection, otherSample.affection) &&
equalOrNull(properties, otherSample.properties);
}
@ -215,7 +215,7 @@ public class Sample implements Comparable<Sample> { // implements java.io.Serial
mergeValues(prev.getID(), "Material_ID", prev.getMaternalID(), next.getMaternalID(), null),
mergeValues(prev.getID(), "Gender", prev.getGender(), next.getGender(), Gender.UNKNOWN),
mergeValues(prev.getID(), "Affection", prev.getAffection(), next.getAffection(), Affection.UNKNOWN),
mergeValues(prev.getID(), "QuantitativeTrait", prev.getQuantitativePhenotype(), next.getQuantitativePhenotype(), UNSET_QT));
mergeValues(prev.getID(), "OtherPhenotype", prev.getOtherPhenotype(), next.getOtherPhenotype(), UNSET_QT));
//mergeValues(prev.getID(), "ExtraProperties", prev.getExtraProperties(), next.getExtraProperties(), Collections.emptyMap()));
}
}

11
public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
View File

@ -8,17 +8,6 @@ import org.broadinstitute.sting.utils.variantcontext.Genotype;
import java.util.*;
/**
* Created by IntelliJ IDEA.
* User: brett
* Date: Jul 26, 2010
* Time: 3:30:09 PM
*
* This class stores and manages sample metadata. This data is encoded in a sample file, which can be included
* in the GATK by the "--samples" argument. This class reads and parses those files.
*
* Although there are a set of public methods for accessing sample data, they aren't used by walkers - they are really
* only used by GenomeAnalysisEngine. An instance of GenomeAnalysisEngine has one SampleDataSource. When a walker
* wants to access sample data, it asks GenomeAnalysis to fetch this data from its SampleDataSource.
*
*/
public class SampleDB {

16
public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java
View File

@ -156,26 +156,26 @@ public class PedReaderUnitTest extends BaseTest {
"fam1 mom granddad2 grandma2 2 2"));
// Quantitative trait
new PedReaderTest("QuantitativeTrait",
new PedReaderTest("OtherPhenotype",
Arrays.asList(
new Sample("s1", "fam1", null, null, Gender.MALE, Affection.QUANTITATIVE, 1.0),
new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.QUANTITATIVE, 10.0)),
new Sample("s1", "fam1", null, null, Gender.MALE, Affection.OTHER, "1.0"),
new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.OTHER, "10.0")),
String.format("%s%n%s",
"fam1 s1 0 0 1 1",
"fam2 s2 0 0 2 10.0"));
new PedReaderTest("QuantitativeTraitWithMissing",
new PedReaderTest("OtherPhenotypeWithMissing",
Arrays.asList(
new Sample("s1", "fam1", null, null, Gender.MALE, Affection.UNKNOWN, Sample.UNSET_QT),
new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.QUANTITATIVE, 10.0)),
new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.OTHER, "10.0")),
String.format("%s%n%s",
"fam1 s1 0 0 1 -9",
"fam2 s2 0 0 2 10.0"));
new PedReaderTest("QuantitativeTraitOnlyInts",
new PedReaderTest("OtherPhenotypeOnlyInts",
Arrays.asList(
new Sample("s1", "fam1", null, null, Gender.MALE, Affection.QUANTITATIVE, 1.0),
new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.QUANTITATIVE, 10.0)),
new Sample("s1", "fam1", null, null, Gender.MALE, Affection.OTHER, "1"),
new Sample("s2", "fam2", null, null, Gender.FEMALE, Affection.OTHER, "10")),
String.format("%s%n%s",
"fam1 s1 0 0 1 1",
"fam2 s2 0 0 2 10"));

21
public/java/test/org/broadinstitute/sting/gatk/samples/SampleUnitTest.java
View File

@ -6,16 +6,13 @@ import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
* Created by IntelliJ IDEA.
* User: brett
* Date: Sep 9, 2010
* Time: 8:21:00 AM
*
*/
public class SampleUnitTest extends BaseTest {
SampleDB db;
static Sample fam1A, fam1B, fam1C;
static Sample s1, s2;
static Sample trait1, trait2, trait3, trait4;
static Sample trait1, trait2, trait3, trait4, trait5;
@BeforeClass
public void init() {
@ -31,7 +28,8 @@ public class SampleUnitTest extends BaseTest {
trait1 = new Sample("t1", db, Affection.AFFECTED, Sample.UNSET_QT);
trait2 = new Sample("t2", db, Affection.UNAFFECTED, Sample.UNSET_QT);
trait3 = new Sample("t3", db, Affection.UNKNOWN, Sample.UNSET_QT);
trait4 = new Sample("t4", db, Affection.QUANTITATIVE, 1.0);
trait4 = new Sample("t4", db, Affection.OTHER, "1.0");
trait5 = new Sample("t4", db, Affection.OTHER, "CEU");
}
/**
@ -47,13 +45,14 @@ public class SampleUnitTest extends BaseTest {
Assert.assertEquals(null, fam1B.getMaternalID());
Assert.assertEquals(Affection.AFFECTED, trait1.getAffection());
Assert.assertEquals(Sample.UNSET_QT, trait1.getQuantitativePhenotype());
Assert.assertEquals(Sample.UNSET_QT, trait1.getOtherPhenotype());
Assert.assertEquals(Affection.UNAFFECTED, trait2.getAffection());
Assert.assertEquals(Sample.UNSET_QT, trait2.getQuantitativePhenotype());
Assert.assertEquals(Sample.UNSET_QT, trait2.getOtherPhenotype());
Assert.assertEquals(Affection.UNKNOWN, trait3.getAffection());
Assert.assertEquals(Sample.UNSET_QT, trait3.getQuantitativePhenotype());
Assert.assertEquals(Affection.QUANTITATIVE, trait4.getAffection());
Assert.assertEquals(1.0, trait4.getQuantitativePhenotype());
Assert.assertEquals(Sample.UNSET_QT, trait3.getOtherPhenotype());
Assert.assertEquals(Affection.OTHER, trait4.getAffection());
Assert.assertEquals("1.0", trait4.getOtherPhenotype());
Assert.assertEquals("CEU", trait5.getOtherPhenotype());
}
@Test()