Class TestCasesIntegrationProteinInteraction
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProteinInteraction
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public class TestCasesIntegrationProteinInteraction extends TestCasesIntegrationBase
Test cases for annotation of protein interaction loci
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
BASE_DIR, debug, ignoreErrors, prefixes, shiftHgvs, SHOW_EVERY, testsDir, testType, verbose
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Constructor Summary
Constructors Constructor Description TestCasesIntegrationProteinInteraction()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_01_within_protein_interactions()
Annotate within protein interactionvoid
test_02_protein_protein_interactions()
Annotate protein-protein interactionsvoid
test_03_protein_protein_interactions_hgvs()
Annotate protein-structural interaction Make sure that the HGVS notation positions (DNA and Protein) are consistent.-
Methods inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
applyTranscript, before, build, buildAndCompare, buildEmbl, buildGeneBank, buildGeneBank, buildGetBuildCmd, buildGff3AndCompare, buildGtfAndCompare, checkHgvs, checkNoChange, checkTranscriptError, compareHgvs, compareHgvs, compareVep, compareVepSO, init, loadSnpEffectPredictor, path, pathClassName, pathMigrate, showTranscripts, showTranscripts, snpEffect, snpEffect, snpEffectCancer
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Method Detail
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test_01_within_protein_interactions
@Test public void test_01_within_protein_interactions()
Annotate within protein interaction
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test_02_protein_protein_interactions
@Test public void test_02_protein_protein_interactions()
Annotate protein-protein interactions
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test_03_protein_protein_interactions_hgvs
@Test public void test_03_protein_protein_interactions_hgvs()
Annotate protein-structural interaction Make sure that the HGVS notation positions (DNA and Protein) are consistent. When the variant is realigned, the protein-interaction annotation should not appear
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