233 lines
9.6 KiB
Java
Executable File
233 lines
9.6 KiB
Java
Executable File
// our package
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package org.broadinstitute.sting.gatk.refdata;
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// the imports for unit testing.
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import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
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import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
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import org.junit.*;
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import static org.junit.Assert.assertTrue;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import java.io.File;
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import java.io.PrintStream;
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import java.io.FileOutputStream;
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import java.io.FileNotFoundException;
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import java.util.Arrays;
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import java.util.ArrayList;
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import net.sf.picard.reference.ReferenceSequenceFile;
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/**
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* Basic unit test for TabularROD
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*
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*/
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public class TabularRODTest extends BaseTest {
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private static ReferenceSequenceFile seq;
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private ReferenceOrderedData ROD;
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private LocationAwareSeekableRODIterator iter;
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@BeforeClass
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public static void init() throws FileNotFoundException {
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// sequence
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seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
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GenomeLocParser.setupRefContigOrdering(seq);
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}
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@Before
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public void setupTabularROD() {
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TabularROD.setDelimiter(TabularROD.DEFAULT_DELIMITER, TabularROD.DEFAULT_DELIMITER_REGEX);
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File file = new File(testDir + "TabularDataTest.dat");
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ROD = new ReferenceOrderedData("tableTest", file, TabularROD.class);
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iter = ROD.iterator();
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}
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@Test
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public void test1() {
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logger.warn("Executing test1");
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RODRecordList oneList = iter.next();
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TabularROD one = (TabularROD)oneList.get(0);
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assertTrue(one.size() == 4);
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assertTrue(one.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 10)));
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assertTrue(one.get("COL1").equals("A"));
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assertTrue(one.get("COL2").equals("B"));
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assertTrue(one.get("COL3").equals("C"));
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}
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@Test
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public void test2() {
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logger.warn("Executing test2");
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RODRecordList oneList = iter.next();
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RODRecordList twoList = iter.next();
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TabularROD one = (TabularROD)oneList.get(0);
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TabularROD two = (TabularROD)twoList.get(0);
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assertTrue(two.size() == 4);
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assertTrue(two.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 20)));
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assertTrue(two.get("COL1").equals("C"));
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assertTrue(two.get("COL2").equals("D"));
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assertTrue(two.get("COL3").equals("E"));
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}
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@Test
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public void test3() {
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logger.warn("Executing test3");
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RODRecordList oneList = iter.next();
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RODRecordList twoList = iter.next();
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RODRecordList threeList = iter.next();
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TabularROD one = (TabularROD)oneList.get(0);
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TabularROD two = (TabularROD)twoList.get(0);
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TabularROD three = (TabularROD)threeList.get(0);
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assertTrue(three.size() == 4);
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assertTrue(three.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 30)));
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assertTrue(three.get("COL1").equals("F"));
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assertTrue(three.get("COL2").equals("G"));
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assertTrue(three.get("COL3").equals("H"));
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}
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@Test
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public void testDone() {
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logger.warn("Executing testDone");
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RODRecordList oneList = iter.next();
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RODRecordList twoList = iter.next();
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RODRecordList threeList = iter.next();
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TabularROD one = (TabularROD)oneList.get(0);
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TabularROD two = (TabularROD)twoList.get(0);
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TabularROD three = (TabularROD)threeList.get(0);
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assertTrue(!iter.hasNext());
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}
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@Test
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public void testSeek() {
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logger.warn("Executing testSeek");
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RODRecordList twoList = iter.seekForward(GenomeLocParser.createGenomeLoc("chrM", 20));
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TabularROD two = (TabularROD)twoList.get(0);
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assertTrue(two.size() == 4);
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assertTrue(two.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 20)));
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assertTrue(two.get("COL1").equals("C"));
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assertTrue(two.get("COL2").equals("D"));
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assertTrue(two.get("COL3").equals("E"));
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}
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@Test
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public void testToString() {
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logger.warn("Executing testToString");
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RODRecordList oneList = iter.next();
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TabularROD one = (TabularROD)oneList.get(0);
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assertTrue(one.toString().equals("chrM:10\tA\tB\tC"));
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}
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// Didn't change the delimiter
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@Test (expected = RuntimeException.class)
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public void testDelim1() {
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File file2 = new File(testDir + "TabularDataTest2.dat");
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ReferenceOrderedData ROD_commas = new ReferenceOrderedData("tableTest", file2, TabularROD.class);
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LocationAwareSeekableRODIterator iter_commas = ROD_commas.iterator();
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logger.warn("Executing testDelim1");
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RODRecordList one2List = iter_commas.next();
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TabularROD one2 = (TabularROD)one2List.get(0);
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assertTrue(one2.size() == 5);
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assertTrue(one2.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 10)));
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assertTrue(one2.get("COL1").equals("A"));
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assertTrue(one2.get("COL2").equals("B"));
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assertTrue(one2.get("COL3").equals("C"));
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assertTrue(one2.get("COL4").equals("1"));
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}
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@Test
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public void testDelim2() {
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TabularROD.setDelimiter(",",",");
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File file2 = new File(testDir + "TabularDataTest2.dat");
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ReferenceOrderedData ROD_commas = new ReferenceOrderedData("tableTest", file2, TabularROD.class);
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LocationAwareSeekableRODIterator iter_commas = ROD_commas.iterator();
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logger.warn("Executing testDelim1");
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RODRecordList one2List = iter_commas.next();
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TabularROD one2 = (TabularROD)one2List.get(0);
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assertTrue(one2.size() == 5);
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assertTrue(one2.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 10)));
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assertTrue(one2.get("COL1").equals("A"));
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assertTrue(one2.get("COL2").equals("B"));
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assertTrue(one2.get("COL3").equals("C"));
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assertTrue(one2.get("COL4").equals("1"));
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}
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@Test
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public void testCreation() {
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logger.warn("Executing testCreation");
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ArrayList<String> header = new ArrayList<String>(Arrays.asList("HEADER", "col1", "col2", "col3"));
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assertTrue(TabularROD.headerString(header).equals("HEADER\tcol1\tcol2\tcol3"));
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String rowData = String.format("%d %d %d", 1, 2, 3);
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TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1), rowData.split(" "));
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System.out.println(">>>>> " + row.toString());
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assertTrue(row.toString().equals("chrM:1\t1\t2\t3"));
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}
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@Test
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public void testCreationAndWriting() throws FileNotFoundException {
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logger.warn("Executing testCreationAndWriting");
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File outputFile = new File(testDir + "testTabularRodOutputTemp.dat");
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PrintStream out = new PrintStream(new FileOutputStream(outputFile));
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ArrayList<String> header = new ArrayList<String>(Arrays.asList("HEADER", "col1", "col2", "col3"));
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out.println(TabularROD.commentString("Hello, created from test"));
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out.println(TabularROD.commentString(""));
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out.println(TabularROD.headerString(header));
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String rowData = String.format("%d %d %d", 1, 2, 3);
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TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1), rowData.split(" "));
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out.println(row.toString());
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rowData = String.format("%d %d %d", 3, 4, 5);
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row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 2), rowData.split(" "));
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out.println(row.toString());
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ReferenceOrderedData ROD_commas = new ReferenceOrderedData("tableTest", outputFile, TabularROD.class);
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LocationAwareSeekableRODIterator iter_commas = ROD_commas.iterator();
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RODRecordList oneList = iter_commas.next();
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TabularROD one = (TabularROD)oneList.get(0);
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assertTrue(one.size() == 4);
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assertTrue(one.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 1)));
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assertTrue(one.get("col1").equals("1"));
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assertTrue(one.get("col2").equals("2"));
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assertTrue(one.get("col3").equals("3"));
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RODRecordList twoList = iter_commas.next();
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TabularROD two = (TabularROD)twoList.get(0);
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assertTrue(two.size() == 4);
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assertTrue(two.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 2)));
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assertTrue(two.get("col1").equals("3"));
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assertTrue(two.get("col2").equals("4"));
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assertTrue(two.get("col3").equals("5"));
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}
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/* @Test (expected=RuntimeException.class )
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public void testBadHeader1() {
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logger.warn("Executing testBadHeader1");
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ArrayList<String> header = new ArrayList<String>();
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TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1));
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}*/
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/* @Test (expected=RuntimeException.class )
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public void testBadHeader2() {
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logger.warn("Executing testBadHeader2");
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ArrayList<String> header = new ArrayList<String>(Arrays.asList("col1", "col2", "col3"));
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TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1));
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}*/
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@Test (expected=RuntimeException.class )
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public void testBadData1() {
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logger.warn("Executing testBadData1");
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ArrayList<String> header = new ArrayList<String>(Arrays.asList("HEADER", "col1", "col2", "col3"));
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assertTrue(TabularROD.headerString(header).equals("HEADER\tcol1\tcol2\tcol3"));
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String rowData = String.format("%d %d %d %d", 1, 2, 3, 4);
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TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1), rowData.split(" "));
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}
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} |