Class TestCasesHgvsProtDup
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup
Test case
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Field Summary
Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, prefixes, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, testType, transcript, verbose
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
test_01()
Test case: p.Gly4_Gln6dup in the sequence MKMGHQQQCC denotes a duplication of amino acids Glycine-4 (Gly, G) to Glutamine-6 (Gln, Q) (i.e.void
test_02()
Reference: http://www.hgvs.org/mutnomen/recs-prot.html#dup duplicating insertions in single amino acid stretches (or short tandem repeats) are described as a duplication, e.g.Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, init, initRand, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon
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Constructor Details
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TestCasesHgvsProtDup
public TestCasesHgvsProtDup()
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Method Details
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test_01
@Test public void test_01()Test case: p.Gly4_Gln6dup in the sequence MKMGHQQQCC denotes a duplication of amino acids Glycine-4 (Gly, G) to Glutamine-6 (Gln, Q) (i.e. MKMGHQGHQQQCC)Reference: http://www.hgvs.org/mutnomen/recs-prot.html#dup
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test_02
@Test public void test_02()Reference: http://www.hgvs.org/mutnomen/recs-prot.html#dup duplicating insertions in single amino acid stretches (or short tandem repeats) are described as a duplication, e.g. a duplicating HQ insertion in the HQ-tandem repeat sequence of MKMGHQHQCC to MKMGHQHQHQCC is described as p.His7_Gln8dup (not p.Gln8_Cys9insHisGln)
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