Class TestCasesIntegrationVariant
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
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public class TestCasesIntegrationVariant extends TestCasesIntegrationBase
Test cases for variants- Author:
- pcingola
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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 TestCasesIntegrationVariant()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_08()
CDS test (CDS = CoDing Sequences) Build CDS form exon sequencesvoid
test_09()
Test SNP effect predictor for a transcriptvoid
test_11()
Test SNP effect predictor: Test UTR distances, Up/Downstream distancesvoid
test_12()
Test SNP effect predictor: Test Splice sitesvoid
test_12_2()
Test SNP effect predictor: Test Splice sites (make sure they are only 2 bases long)void
test_19()
Test SNP effect predictor: Test start codon gainedvoid
test_20()
Test SNP effect predictor: Test start codon gained (reverse strand)void
test_21()
Test SNP effect predictor for a transcript (Insertions)void
test_21_2()
Test SNP effect predictor for a transcript (Insertions)void
test_21_3()
Test SNP effect predictor for a transcript (Insertions)void
test_22()
Read file test: Should throw an exception (chromosome not found)void
test_23_MNP_on_exon_edge()
Test SNP effect predictor for a transcript (Insertions)void
test_24_delete_exon_utr()
Test SNP effect predictor for a transcript (Insertions)void
test_25_exon_bases()
void
test_26_chr15_78909452()
Test SNP effect predictor for a transcript (Insertions)void
test_28_Splice_mm37_ENSMUSG00000005763()
Splice site: Bug reported by Wang, Xushengvoid
test_29_Intergenic_in_Gene()
Test effect when hits a gene, but not any transcript within a gene.void
test_30_RareAa()
Rare Amino acidvoid
test_31_CodonTable()
MT chromo Effectusing an alternative codon table: Codon change : atA / atG Standard codon table : Ile / Met => NON_SYNONYMOUS Mithocondria codon table: Met / Met => SYNONYMOUSvoid
test_32_StartGained()
Start gainedvoid
test_33_StartGained_NOT()
Not start gainedvoid
test_34_StartGained()
Start gainedvoid
test_35_StartGained_NOT()
Not start gainedvoid
test_36_EffectImpact()
Make sure all variant effects have appropriate impactsvoid
test_38_NON_SYNONYMOUS_START()
Test-
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_08
@Test public void test_08()
CDS test (CDS = CoDing Sequences) Build CDS form exon sequences
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test_09
@Test public void test_09()
Test SNP effect predictor for a transcript
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test_11
@Test public void test_11()
Test SNP effect predictor: Test UTR distances, Up/Downstream distances
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test_12
@Test public void test_12()
Test SNP effect predictor: Test Splice sites
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test_12_2
@Test public void test_12_2()
Test SNP effect predictor: Test Splice sites (make sure they are only 2 bases long)
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test_19
@Test public void test_19()
Test SNP effect predictor: Test start codon gained
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test_20
@Test public void test_20()
Test SNP effect predictor: Test start codon gained (reverse strand)
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test_21
@Test public void test_21()
Test SNP effect predictor for a transcript (Insertions)
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test_21_2
@Test public void test_21_2()
Test SNP effect predictor for a transcript (Insertions)
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test_21_3
@Test public void test_21_3()
Test SNP effect predictor for a transcript (Insertions)
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test_22
@Test public void test_22()
Read file test: Should throw an exception (chromosome not found)
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test_23_MNP_on_exon_edge
@Test public void test_23_MNP_on_exon_edge()
Test SNP effect predictor for a transcript (Insertions)
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test_24_delete_exon_utr
@Test public void test_24_delete_exon_utr()
Test SNP effect predictor for a transcript (Insertions)
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test_25_exon_bases
@Test public void test_25_exon_bases()
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test_26_chr15_78909452
@Test public void test_26_chr15_78909452()
Test SNP effect predictor for a transcript (Insertions)
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test_28_Splice_mm37_ENSMUSG00000005763
@Test public void test_28_Splice_mm37_ENSMUSG00000005763()
Splice site: Bug reported by Wang, Xusheng
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test_29_Intergenic_in_Gene
@Test public void test_29_Intergenic_in_Gene()
Test effect when hits a gene, but not any transcript within a gene. This is an extremely weird case, might be an annotation problem.
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test_30_RareAa
@Test public void test_30_RareAa()
Rare Amino acid
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test_31_CodonTable
@Test public void test_31_CodonTable()
MT chromo Effectusing an alternative codon table: Codon change : atA / atG Standard codon table : Ile / Met => NON_SYNONYMOUS Mithocondria codon table: Met / Met => SYNONYMOUS
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test_32_StartGained
@Test public void test_32_StartGained()
Start gained
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test_33_StartGained_NOT
@Test public void test_33_StartGained_NOT()
Not start gained
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test_34_StartGained
@Test public void test_34_StartGained()
Start gained
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test_35_StartGained_NOT
@Test public void test_35_StartGained_NOT()
Not start gained
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test_36_EffectImpact
@Test public void test_36_EffectImpact()
Make sure all variant effects have appropriate impacts
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test_38_NON_SYNONYMOUS_START
@Test public void test_38_NON_SYNONYMOUS_START()
Test
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