zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodTest.java

244 lines
13 KiB
Java
Executable File
Raw Blame History

//package org.broadinstitute.sting.gatk.refdata;
//
//import org.broadinstitute.sting.BaseTest;
//import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
//import org.broadinstitute.sting.utils.StingException;
//import org.broadinstitute.sting.utils.GenomeLocParser;
//import org.broadinstitute.sting.utils.GenomeLoc;
//import org.junit.BeforeClass;
//import org.junit.Test;
//import org.junit.Assert;
//
//import java.io.File;
//import java.io.FileNotFoundException;
//import java.io.BufferedReader;
//import java.io.FileReader;
//import java.util.*;
//
///**
// * Created by IntelliJ IDEA.
// * User: Ghost
// * Date: Jan 22, 2010
// * Time: 11:27:33 PM
// * To change this template use File | Settings | File Templates.
// */
//public class PlinkRodTest extends BaseTest {
// private static IndexedFastaSequenceFile seq;
//
// @BeforeClass
// public static void beforeTests() {
// try {
// seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
// } catch (FileNotFoundException e) {
// throw new StingException("unable to load the sequence dictionary");
// }
// GenomeLocParser.setupRefContigOrdering(seq);
//
// }
//
// public BufferedReader openFile(String filename) {
// try {
// return new BufferedReader(new FileReader(filename));
// } catch (FileNotFoundException e) {
// throw new StingException("Couldn't open file " + filename);
// }
//
// }
//
// @Test
// public void testStandardPedFile() {
// PlinkRod rod = new PlinkRod("test");
// try {
// rod.initialize( new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_test.ped") );
// } catch ( FileNotFoundException e ) {
// throw new StingException("test file for testStandardPedFile() does not exist",e);
// }
//
// // test that the sample names are correct
//
// List<String> rodNames = rod.getVariantSampleNames();
// List<String> expectedNames = Arrays.asList("NA12887","NAMELY","COWBA");
//
// Assert.assertEquals("That there are as many samples in the rod as in the expected list",expectedNames.size(),rodNames.size());
//
// boolean namesCorrect = true;
// for ( int i = 0; i < expectedNames.size(); i++ ) {
// namesCorrect = namesCorrect && ( rodNames.get(i).equals(expectedNames.get(i)) );
// }
//
// Assert.assertTrue("That the names are correct and in the proper order",namesCorrect);
//
// // test that rod can be iterated over
//
// ArrayList<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
// ArrayList<ArrayList<String>> sampleNamesInRod = new ArrayList<ArrayList<String>>();
// ArrayList<GenomeLoc> lociInRod = new ArrayList<GenomeLoc>();
// do {
// genotypesInRod.add(rod.getGenotypes());
// sampleNamesInRod.add(rod.getVariantSampleNames());
// lociInRod.add(rod.getLocation());
// } while ( rod.parseLine(null,null) );
//
// Assert.assertEquals("That there are three SNPs in the ROD",3,genotypesInRod.size());
//
// ArrayList<Genotype> snp1 = genotypesInRod.get(0);
// ArrayList<Genotype> snp3 = genotypesInRod.get(2);
//
// Assert.assertEquals("That there are three Genotypes in SNP 1",3,snp1.size());
// Assert.assertEquals("That there are three samples in SNP 2", 3, sampleNamesInRod.get(1).size());
// Assert.assertEquals("That there are three Genotypes in SNP 3",3,snp3.size());
//
//
// List<Allele> snp1_individual3_alleles = snp1.get(2).getAlleles();
// List<Allele> snp3_individual2_alleles = snp3.get(1).getAlleles();
//
// String alleleStr1 = snp1_individual3_alleles.get(0).getBases()+snp1_individual3_alleles.get(1).getBases();
// String alleleStr2 = snp3_individual2_alleles.get(0).getBases()+snp3_individual2_alleles.get(1).getBases();
//
// Assert.assertEquals("That the third genotype of snp 1 is correctly no-call","00",alleleStr1);
// Assert.assertEquals("That the second genotype of snp 3 is correctly G G","GG",alleleStr2);
//
// boolean name2isSame = true;
//
// for ( ArrayList<String> names : sampleNamesInRod ) {
// name2isSame = name2isSame && names.get(1).equals("NAMELY");
// }
//
// Assert.assertTrue("That the second name of all the genotypes is the same and is correct",name2isSame);
//
// // test that the loci are correctly parsed and in order
//
// List<String> expectedLoci = Arrays.asList("1:123456","2:13274","3:11111");
// boolean lociCorrect = true;
// for ( int i = 0; i < 3; i ++ ) {
// lociCorrect = lociCorrect && lociInRod.get(i).toString().equals(expectedLoci.get(i));
// }
// }
//
// @Test
// public void testStandardPedFileWithIndels() {
// PlinkRod rod = new PlinkRod("test");
// try {
// rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/standard_plink_with_indels.ped") );
// } catch ( FileNotFoundException e) {
// throw new StingException("Test file for testStandardPedFileWithIndels() could not be found", e);
// }
//
// // Iterate through the rod
//
// List<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
// ArrayList<ArrayList<String>> sampleNamesInRod = new ArrayList<ArrayList<String>>();
// ArrayList<GenomeLoc> lociInRod = new ArrayList<GenomeLoc>();
// ArrayList<Boolean> snpSites = new ArrayList<Boolean>();
// do {
// genotypesInRod.add(rod.getGenotypes());
// sampleNamesInRod.add(rod.getVariantSampleNames());
// lociInRod.add(rod.getLocation());
// snpSites.add(rod.variantIsSNP());
// } while ( rod.parseLine(null,null) );
//
// boolean snpOrder = true;
// List<Boolean> expectedOrder = Arrays.asList(true,false,true,false);
// for ( int i = 0; i < 4; i ++ ) {
// snpOrder = snpOrder && ( expectedOrder.get(i) == snpSites.get(i) );
// }
//
// Assert.assertTrue("That the variant type order is as expected", snpOrder);
// Assert.assertTrue("That the second genotype of second variant is not a point mutation", ! genotypesInRod.get(1).get(1).isPointGenotype() );
// Assert.assertTrue("That the second genotype of fourth variant is not a point mutation", ! genotypesInRod.get(3).get(1).isPointGenotype() );
// Assert.assertTrue("That the second genotype of fourth variant is homozygous", genotypesInRod.get(3).get(1).isHom());
// Assert.assertTrue("That the fourth genotype of fourth variant is heterozygous",genotypesInRod.get(3).get(3).isHet());
// Assert.assertEquals("That the reference deletion genotype has the correct string", "ATTTAT",genotypesInRod.get(3).get(2).getAlleles().get(0).getBases());
// Assert.assertEquals("That the insertion bases are correct","CTC",genotypesInRod.get(1).get(2).getAlleles().get(0).getBases());
// Assert.assertEquals("That the snp bases are correct","GC",genotypesInRod.get(2).get(2).getAlleles().get(0).getBases()+genotypesInRod.get(2).get(2).getAlleles().get(1).getBases());
// }
//
// @Test
// public void testBinaryPedFileNoIndels() {
// PlinkRod rod = new PlinkRod("binaryTest1");
// try {
// rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_noindel_test.bed"));
// } catch (FileNotFoundException e) {
// throw new StingException("Test file for testBinaryPedFileNoIndels() could not be found",e);
// }
//
// // iterate through the ROD and get stuff
// ArrayList<GenomeLoc> lociInRod = new ArrayList<GenomeLoc>();
// ArrayList<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
// ArrayList<ArrayList<String>> samplesInRod = new ArrayList<ArrayList<String>>();
//
// do {
// lociInRod.add(rod.getLocation());
// genotypesInRod.add(rod.getGenotypes());
// samplesInRod.add(rod.getVariantSampleNames());
// } while ( rod.parseLine(null,null) );
//
// List<String> expecLoc = Arrays.asList("1:123456","1:14327877","2:22074511","3:134787","3:178678","4:829645","4:5234132","12:1268713");
//
// for ( int i = 0; i < expecLoc.size(); i ++ ) {
// Assert.assertEquals("That locus "+(i+1)+" in the rod is correct", expecLoc.get(i), lociInRod.get(i).toString());
// }
//
// List<String> expecAlleles = Arrays.asList("AA","AA","AA","GG","GG","GG","AA","TA","TT","CC","CC","GC","TC","CC","TT",
// "GG","GG","AG","TT","CC","CT","TG","GG","GG");
// List<Boolean> expecHet = Arrays.asList(false,false,false,false,false,false,false,true,false,false,false,true,true,false,
// false,false,false,true,false,false,true,true,false,false);
// List<String> expecName = Arrays.asList("NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000",
// "NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000","NA12878","NA12890","NA07000",
// "NA12878","NA12890","NA07000");
// int snpNo = 1;
// int indiv = 1;
// int alleleOffset = 0;
// for ( ArrayList<Genotype> snp : genotypesInRod ) {
// for ( Genotype gen : snp ) {
// String alStr = gen.getAlleles().get(0).getBases()+gen.getAlleles().get(1).getBases();
// Assert.assertEquals("That the allele of person "+indiv+" for snp "+snpNo+" is correct "+
// "(allele offset "+alleleOffset+")", expecAlleles.get(alleleOffset),alStr);
// Assert.assertEquals("That the genotype of person "+indiv+" for snp "+snpNo+" is properly set", expecHet.get(alleleOffset),gen.isHet());
// Assert.assertEquals("That the name of person "+indiv+" for snp "+snpNo+" is correct", expecName.get(alleleOffset),samplesInRod.get(snpNo-1).get(indiv-1));
// indiv++;
// alleleOffset++;
// }
// indiv = 1;
// snpNo++;
// }
// }
//
// @Test
// public void testIndelBinary() {
// PlinkRod rod = new PlinkRod("binaryTest2");
// try {
// rod.initialize(new File("/humgen/gsa-hpprojects/GATK/data/Validation_Data/test/plink_rod_test/binary_indel_test.bed"));
// } catch (FileNotFoundException e) {
// throw new StingException("Test file for testBinaryPedFileNoIndels() could not be found",e);
// }
//
// ArrayList<ArrayList<Genotype>> genotypesInRod = new ArrayList<ArrayList<Genotype>>();
// do {
// genotypesInRod.add(rod.getGenotypes());
// } while ( rod.parseLine(null,null) );
//
// List<String> expecAlleles = Arrays.asList("ACCA","","ACCAACCA","GGGG","GG","","AA","TA","00","","CCTCCT","CCT",
// "TC","CC","TT","GG","GG","AG","","CTTGCTTG","CTTG","TG","GG","GG");
// List<Boolean> expecDeletion = Arrays.asList(false,false,false,false,false,false,false,false,false,true,false,true,
// false,false,false,false,false,false,true,false,true,false,false,false);
// List<Boolean> expecInsertion = Arrays.asList(true,false,true,true,true,false,false,false,false,false,false,false,
// false,false,false,false,false,false,false,false,false,false,false,false);
//
// int al = 0;
// for ( ArrayList<Genotype> snp : genotypesInRod ) {
// for ( Genotype gen : snp ) {
// String alStr = gen.getAlleles().get(0).getBases()+gen.getAlleles().get(1).getBases();
// Allele firstAl = gen.getAlleles().get(0);
// Allele secondAl = gen.getAlleles().get(1);
// boolean isInsertion = ( firstAl.getType() == Allele.AlleleType.INSERTION || secondAl.getType() == Allele.AlleleType.INSERTION );
// boolean isDeletion = ( firstAl.getType() == Allele.AlleleType.DELETION || secondAl.getType() == Allele.AlleleType.DELETION );
// Assert.assertEquals("That the indel file has the correct alleles for genotype "+al,expecAlleles.get(al), alStr);
// Assert.assertEquals("That the insertion property of genotype "+al+" is correct",expecInsertion.get(al),isInsertion);
// Assert.assertEquals("That the deletion property of genotype "+al+" is correct", expecDeletion.get(al), isDeletion);
// al++;
// }
// }
// }
//}
Reference in New Issue View Git Blame Copy Permalink