Class TestCasesHgvsProtDup
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup
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public class TestCasesHgvsProtDup extends TestCasesBase
Test case
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, transcript, verbose
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Constructor Summary
Constructors Constructor Description TestCasesHgvsProtDup()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.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, prependSequenceToFirstExon, showTranscripts
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Method Detail
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test_01
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
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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