Class TestCasesIntegrationProteinInteraction
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProteinInteraction
Test cases for annotation of protein interaction loci
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Field Summary
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
Annotate within protein interactionvoid
Annotate protein-protein interactionsvoid
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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Constructor Details
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TestCasesIntegrationProteinInteraction
public TestCasesIntegrationProteinInteraction()
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Method Details
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test_01_within_protein_interactions
@Test public void test_01_within_protein_interactions()Annotate within protein interaction -
test_02_protein_protein_interactions
@Test public void test_02_protein_protein_interactions()Annotate protein-protein interactions -
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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