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fix: use dataProvider for integration tests
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.../java/org/broadinstitute/hellbender/tools/walkers/conversion/GtfToBedIntegrationTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,148 +1,78 @@ | ||
| package org.broadinstitute.hellbender.tools.walkers.conversion; | ||
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| import org.broadinstitute.hellbender.CommandLineProgramTest; | ||
| import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; | ||
| import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; | ||
| import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; | ||
| import org.testng.Assert; | ||
| import org.testng.annotations.DataProvider; | ||
| import org.testng.annotations.Test; | ||
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| import java.io.*; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| public class GtfToBedIntegrationTest extends CommandLineProgramTest { | ||
| final File outputFile = createTempFile("outputBed", ".bed"); | ||
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| private static final File mapk1 = new File(ConversionTestUtils.getMapk1Gtf()); | ||
| private static final File decoys = new File(ConversionTestUtils.getDecoySampleGtf()); | ||
| private static final File manyTranscripts = new File(ConversionTestUtils.getManyTranscriptsGtf()); | ||
| private static final File mouse = new File(ConversionTestUtils.getMouseGtf()); | ||
| private static final File mouseDictionary = new File(ConversionTestUtils.getMouseDict()); | ||
| private static final File dictionary = new File(ConversionTestUtils.getReferenceDict()); | ||
| private static final File expectedDecoysGeneBed = new File(ConversionTestUtils.getDecoySamplesGeneBed()); | ||
| private static final File expectedDecoysTranscriptBed = new File(ConversionTestUtils.getDecoySamplesTranscriptBed()); | ||
| private static final File expectedMapk1GeneBed = new File(ConversionTestUtils.getMapk1GeneBed()); | ||
| private static final File expectedMapk1TranscriptBed = new File(ConversionTestUtils.getMapk1TranscriptBed()); | ||
| private static final File expectedManyTranscriptsBed = new File (ConversionTestUtils.getManyTranscriptsBed()); | ||
| private static final File expectedNotBasicBed = new File(ConversionTestUtils.getNotBasicBed()); | ||
| private static final File expectedMouseBed = new File(ConversionTestUtils.getMouseBed()); | ||
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| // tests specifically mapk1 gene | ||
| @Test | ||
| public void testMapk1Gene() throws IOException { | ||
| runMapk1(false); | ||
| } | ||
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| // tests transcripts in mapk1 gene | ||
| @Test | ||
| public void testMapk1Transcript() throws IOException { | ||
| runMapk1(true); | ||
| } | ||
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| // tests a sample of decoy genes (gene) - decoy = any gene that doesn't start with "chr" | ||
| @Test | ||
| public void testDecoyGenes() throws IOException { | ||
| runDecoySample(false); | ||
| } | ||
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| // tests a sample of decoy genes (transcript) | ||
| @Test | ||
| public void testDecoyTranscripts() throws IOException { | ||
| runDecoySample(true); | ||
| } | ||
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| // tests a gene with many transcripts and a gene in another chr | ||
| @Test | ||
| public void testManyTranscripts() throws IOException { | ||
| runManyTranscripts(); | ||
| } | ||
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| @Test | ||
| public void testNotBasic() throws IOException { | ||
| runNotBasic(); | ||
| } | ||
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| @Test | ||
| public void testMouse() throws IOException { | ||
| runMouse(); | ||
| } | ||
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| private void runMapk1(boolean transcript) throws IOException { | ||
| final ArgumentsBuilder argsBuilder = new ArgumentsBuilder() | ||
| .add(GtfToBed.INPUT_LONG_NAME, mapk1) | ||
| .add(GtfToBed.SEQUENCE_DICTIONARY_LONG_NAME, dictionary) | ||
| .add(GtfToBed.SORT_BY_TRANSCRIPT_LONG_NAME, transcript) | ||
| .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, true) | ||
| .addOutput(outputFile); | ||
| runCommandLine(argsBuilder); | ||
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| if (transcript) { | ||
| Assert.assertEquals(countLines(outputFile), 3); | ||
| IntegrationTestSpec.assertEqualTextFiles(expectedMapk1TranscriptBed, outputFile); | ||
| } else { | ||
| Assert.assertEquals(countLines(outputFile), 1); | ||
| IntegrationTestSpec.assertEqualTextFiles(expectedMapk1GeneBed, outputFile); | ||
| } | ||
| } | ||
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| private void runDecoySample(boolean transcript) throws IOException { | ||
| final ArgumentsBuilder argsBuilder = new ArgumentsBuilder() | ||
| .add(GtfToBed.INPUT_LONG_NAME, decoys) | ||
| .add(GtfToBed.SEQUENCE_DICTIONARY_LONG_NAME, dictionary) | ||
| .add(GtfToBed.SORT_BY_TRANSCRIPT_LONG_NAME, transcript) | ||
| .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, true) | ||
| .addOutput(outputFile); | ||
| countLines(outputFile); | ||
| runCommandLine(argsBuilder); | ||
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| if (transcript) { | ||
| Assert.assertEquals(countLines(outputFile), 20); | ||
| IntegrationTestSpec.assertEqualTextFiles(expectedDecoysTranscriptBed, outputFile); | ||
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| } else { | ||
| Assert.assertEquals(countLines(outputFile), 19); | ||
| IntegrationTestSpec.assertEqualTextFiles(expectedDecoysGeneBed, outputFile); | ||
| private static final String mapk1 = ConversionTestUtils.getMapk1Gtf(); | ||
| private static final String decoys = ConversionTestUtils.getDecoySampleGtf(); | ||
| private static final String manyTranscripts = ConversionTestUtils.getManyTranscriptsGtf(); | ||
| private static final String mouse = ConversionTestUtils.getMouseGtf(); | ||
| private static final String mouseDictionary = ConversionTestUtils.getMouseDict(); | ||
| private static final String dictionary = ConversionTestUtils.getReferenceDict(); | ||
| private static final String expectedDecoysGeneBed = ConversionTestUtils.getDecoySamplesGeneBed(); | ||
| private static final String expectedDecoysTranscriptBed = ConversionTestUtils.getDecoySamplesTranscriptBed(); | ||
| private static final String expectedMapk1GeneBed = ConversionTestUtils.getMapk1GeneBed(); | ||
| private static final String expectedMapk1TranscriptBed = ConversionTestUtils.getMapk1TranscriptBed(); | ||
| private static final String expectedManyTranscriptsBed = ConversionTestUtils.getManyTranscriptsBed(); | ||
| private static final String expectedNotBasicBed = ConversionTestUtils.getNotBasicBed(); | ||
| private static final String expectedMouseBed = ConversionTestUtils.getMouseBed(); | ||
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| private static class GtfToBedTest { | ||
| final String input; | ||
| final String SD; | ||
| final String transcript; | ||
| final String basic; | ||
| final String expected; | ||
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| private GtfToBedTest(String input, String SD, String transcript, String basic, String expected) { | ||
| this.input = input; | ||
| this.SD = SD; | ||
| this.transcript = transcript; | ||
| this.basic = basic; | ||
| this.expected = expected; | ||
| } | ||
| } | ||
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| private void runManyTranscripts() throws IOException { | ||
| final ArgumentsBuilder argsBuilder = new ArgumentsBuilder() | ||
| .add(GtfToBed.INPUT_LONG_NAME, manyTranscripts) | ||
| .add(GtfToBed.SEQUENCE_DICTIONARY_LONG_NAME, dictionary) | ||
| .add(GtfToBed.SORT_BY_TRANSCRIPT_LONG_NAME, true) | ||
| .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, true) | ||
| .addOutput(outputFile); | ||
| runCommandLine(argsBuilder); | ||
| IntegrationTestSpec.assertEqualTextFiles(expectedManyTranscriptsBed, outputFile); | ||
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| } | ||
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| private void runNotBasic() throws IOException { | ||
| final ArgumentsBuilder argsBuilder = new ArgumentsBuilder() | ||
| .add(GtfToBed.INPUT_LONG_NAME, manyTranscripts) | ||
| .add(GtfToBed.SEQUENCE_DICTIONARY_LONG_NAME, dictionary) | ||
| .add(GtfToBed.SORT_BY_TRANSCRIPT_LONG_NAME, true) | ||
| .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, false) | ||
| .addOutput(outputFile); | ||
| runCommandLine(argsBuilder); | ||
| IntegrationTestSpec.assertEqualTextFiles(expectedNotBasicBed, outputFile); | ||
| @DataProvider(name = "GtfToBedTestProvider") | ||
| public Object[][] equalRangeData() { | ||
| List<Object[]> tests = new ArrayList<>(); | ||
| tests.add(new Object[]{new GtfToBedTest(mapk1, dictionary, String.valueOf(false), String.valueOf(true), expectedMapk1GeneBed)}); | ||
| tests.add(new Object[]{new GtfToBedTest(mapk1, dictionary, String.valueOf(true), String.valueOf(true), expectedMapk1TranscriptBed)}); | ||
| tests.add(new Object[]{new GtfToBedTest(decoys, dictionary, String.valueOf(false), String.valueOf(true), expectedDecoysGeneBed)}); | ||
| tests.add(new Object[]{new GtfToBedTest(decoys, dictionary, String.valueOf(true), String.valueOf(true), expectedDecoysTranscriptBed)}); | ||
| tests.add(new Object[]{new GtfToBedTest(manyTranscripts, dictionary, String.valueOf(true), String.valueOf(true), expectedManyTranscriptsBed)}); | ||
| tests.add(new Object[]{new GtfToBedTest(manyTranscripts, dictionary, String.valueOf(true), String.valueOf(false), expectedNotBasicBed)}); | ||
| tests.add(new Object[]{new GtfToBedTest(mouse, mouseDictionary, String.valueOf(true), String.valueOf(false), expectedMouseBed)}); | ||
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| return tests.toArray(new Object[][]{}); | ||
| } | ||
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| private void runMouse() throws IOException { | ||
| final ArgumentsBuilder argsBuilder = new ArgumentsBuilder() | ||
| .add(GtfToBed.INPUT_LONG_NAME, mouse) | ||
| .add(GtfToBed.SEQUENCE_DICTIONARY_LONG_NAME, mouseDictionary) | ||
| .add(GtfToBed.SORT_BY_TRANSCRIPT_LONG_NAME, true) | ||
| .add(GtfToBed.SORT_BY_BASIC_LONG_NAME, false) | ||
| .addOutput(outputFile); | ||
| runCommandLine(argsBuilder); | ||
| IntegrationTestSpec.assertEqualTextFiles(expectedMouseBed, outputFile); | ||
| } | ||
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| private int countLines(File file) throws IOException { | ||
| BufferedReader reader = new BufferedReader(new FileReader(file)); | ||
| int lines = 0; | ||
| while (reader.readLine() != null) { | ||
| lines++; | ||
| } | ||
| return lines; | ||
| @Test(dataProvider = "GtfToBedTestProvider") | ||
| public void testGtfToBed(GtfToBedTest params) throws IOException { | ||
| final File outputFile = createTempFile("outputBed", ".bed"); | ||
| final ArrayList<String> args = new ArrayList<>(); | ||
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| args.add("--" + GtfToBed.INPUT_LONG_NAME); | ||
| args.add(new File (params.input).getAbsolutePath()); | ||
| args.add("--" + StandardArgumentDefinitions.SEQUENCE_DICTIONARY_NAME); | ||
| args.add(new File (params.SD).getAbsolutePath()); | ||
| args.add("--" + GtfToBed.SORT_BY_TRANSCRIPT_LONG_NAME); | ||
| args.add(params.transcript); | ||
| args.add("--" + GtfToBed.SORT_BY_BASIC_LONG_NAME); | ||
| args.add(params.basic); | ||
| args.add("--" + StandardArgumentDefinitions.OUTPUT_LONG_NAME); | ||
| args.add(outputFile.getAbsolutePath()); | ||
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| runCommandLine(args); | ||
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| IntegrationTestSpec.assertEqualTextFiles(new File(params.expected), outputFile); | ||
| } | ||
| } |