Class TestCasesBase
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
- Direct Known Subclasses:
TestCasesAnn
,TestCasesAnnParse
,TestCasesBaseApply
,TestCasesBuild
,TestCasesCds
,TestCasesDels
,TestCasesDnaSequence
,TestCasesEffectCollapse
,TestCasesEffectCollapse2
,TestCasesFasta
,TestCasesFileIndexChrPos
,TestCasesHgvs
,TestCasesHgvsDnaDup
,TestCasesHgvsDnaDupNegative
,TestCasesHgvsProtDup
,TestCasesIns
,TestCasesIntergenic
,TestCasesIntervals
,TestCasesIntervalVariant
,TestCasesIntStats
,TestCasesJaspar
,TestCasesMnps
,TestCasesSeekableReader
,TestCasesSequenceIndexer
,TestCasesSnps
,TestCasesSpliceRegion
,TestCasesSpliceSite
,TestCasesStructuralDel
,TestCasesStructuralDup
,TestCasesStructuralInv
,TestCasesVariantRealignment
,TestCasesVcf
,TestCasesZzz
Base class for some test cases
- Author:
- pcingola
-
Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
static final String
protected char[]
protected String
protected Chromosome
protected CodonTable
protected Config
protected boolean
protected Gene
protected Genome
protected String
protected int
protected int
protected int
protected int
protected int
protected boolean
protected boolean
protected Random
protected int
protected boolean
protected SnpEffectPredictor
protected int
protected int
protected int
protected String
protected Transcript
protected boolean
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
after()
void
before()
void
checkApply
(Variant variant, Variant.VariantType varType, String expectedCds, String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End) Apply a variant to a transcript and check resulting CDS sequence, protein sequence and exon coordinatesvoid
checkApplyDel
(Variant variant, String expectedCds, String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End) void
checkApplyIns
(Variant variant, String expectedCds, String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End) void
checkApplyMixed
(Variant variant, String expectedCds, String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End) void
checkApplyMnp
(Variant variant, String expectedCds, String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End) void
checkApplySnp
(Variant variant, String expectedCds, String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End) protected void
checkEffect
(Variant variant, EffectType effectExpected) protected void
checkEffect
(Variant variant, EffectType effectExpected, EffectType effectNotExpected, VariantEffect.EffectImpact impact) protected EffFormatVersion
formatVersion
(String vcfFileName) Get file's format versionprotected boolean
Is effectExpected included in effStr (many effects delimited by '&'protected void
init()
protected void
initRand()
protected void
protected void
initSnpEffPredictor
(Gene[] genesToAdd) Create a predictor For the default parameters the first predictor created has only one transcript: 1:880-1001, strand: +, id:transcript_0, Protein Exons: 1:880-1001 'exon_0_0', rank: 1, frame: ., sequence: taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcggga CDS : taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcgggac Protein : *PHMISTVEEKHLTPIEQDLFRNTLYR*PIYLIPHIYFIG?protected String
protected void
prependSequenceToFirstExon
(String prepend) Prepend first's exons sequence with a given one
-
Field Details
-
BASE_DIR
- See Also:
-
debug
protected boolean debug -
verbose
protected boolean verbose -
randSeed
protected int randSeed -
genomeName
-
addUtrs
protected boolean addUtrs -
onlyPlusStrand
protected boolean onlyPlusStrand -
onlyMinusStrand
protected boolean onlyMinusStrand -
shiftHgvs
protected boolean shiftHgvs -
numGenes
protected int numGenes -
maxGeneLen
protected int maxGeneLen -
maxTranscripts
protected int maxTranscripts -
maxExons
protected int maxExons -
minExons
protected int minExons -
spliceRegionExonSize
protected int spliceRegionExonSize -
spliceRegionIntronMin
protected int spliceRegionIntronMin -
spliceRegionIntronMax
protected int spliceRegionIntronMax -
rand
-
config
-
genome
-
chromosome
-
gene
-
transcript
-
snpEffectPredictor
-
chromoSequence
-
chromoBases
protected char[] chromoBases -
codonTable
-
testType
-
prefixes
-
-
Constructor Details
-
TestCasesBase
public TestCasesBase()
-
-
Method Details
-
after
@AfterEach public void after() -
before
@BeforeEach public void before() -
checkApply
public void checkApply(Variant variant, Variant.VariantType varType, String expectedCds, String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End) Apply a variant to a transcript and check resulting CDS sequence, protein sequence and exon coordinates -
checkApplyDel
-
checkApplyIns
-
checkApplyMixed
-
checkApplyMnp
-
checkApplySnp
-
checkEffect
-
checkEffect
protected void checkEffect(Variant variant, EffectType effectExpected, EffectType effectNotExpected, VariantEffect.EffectImpact impact) -
formatVersion
Get file's format version -
hasEffect
Is effectExpected included in effStr (many effects delimited by '&' -
init
protected void init() -
initRand
protected void initRand() -
initSnpEffPredictor
protected void initSnpEffPredictor() -
initSnpEffPredictor
Create a predictor For the default parameters the first predictor created has only one transcript: 1:880-1001, strand: +, id:transcript_0, Protein Exons: 1:880-1001 'exon_0_0', rank: 1, frame: ., sequence: taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcggga CDS : taaccccatatgattagtacggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgatgaccgatttatttgattccccacatttatttcatcgggac Protein : *PHMISTVEEKHLTPIEQDLFRNTLYR*PIYLIPHIYFIG? -
path
-
pathClassName
-
prependSequenceToFirstExon
Prepend first's exons sequence with a given one
-