Package org.snpeff.snpEffect.testCases.unity

Class TestCasesBase

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesBase

Direct Known Subclasses:

TestCasesAnn, TestCasesBaseApply, TestCasesCds, TestCasesDels, TestCasesEffectCollapse, TestCasesEffectCollapse2, TestCasesHgvs, TestCasesHgvsDnaDup, TestCasesHgvsDnaDupNegative, TestCasesHgvsProtDup, TestCasesIns, TestCasesIntergenic, TestCasesIntervalVariant, TestCasesMnps, TestCasesSnps, TestCasesSpliceRegion, TestCasesSpliceSite, TestCasesStructuralDel, TestCasesStructuralDup, TestCasesStructuralInv, TestCasesVariantRealignment, TestCasesVcf

public class TestCasesBase
extends java.lang.Object

Base class for some test cases

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	addUtrs
protected char[]	chromoBases
protected java.lang.String	chromoSequence
protected Chromosome	chromosome
protected CodonTable	codonTable
protected Config	config
protected boolean	debug
protected Gene	gene
protected Genome	genome
protected java.lang.String	genomeName
protected int	maxExons
protected int	maxGeneLen
protected int	maxTranscripts
protected int	minExons
protected int	numGenes
protected boolean	onlyMinusStrand
protected boolean	onlyPlusStrand
protected java.util.Random	rand
protected int	randSeed
protected boolean	shiftHgvs
protected SnpEffectPredictor	snpEffectPredictor
protected int	spliceRegionExonSize
protected int	spliceRegionIntronMax
protected int	spliceRegionIntronMin
protected Transcript	transcript
protected boolean	verbose

Constructor Summary

Constructors

Constructor	Description
TestCasesBase()

Method Summary

Modifier and Type	Method	Description
void	after()
void	before()
void	checkApply(Variant variant, Variant.VariantType varType, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)	Apply a variant to a transcript and check resulting CDS sequence, protein sequence and exon coordinates
void	checkApplyDel(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
void	checkApplyIns(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
void	checkApplyMixed(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
void	checkApplyMnp(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
void	checkApplySnp(Variant variant, java.lang.String expectedCds, java.lang.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(java.lang.String vcfFileName)	Get file's format version
protected boolean	hasEffect(java.lang.String effectExpected, java.lang.String effStr)	Is effectExpected included in effStr (many effects delimited by '&'
protected void	init()
protected void	initRand()
protected void	initSnpEffPredictor()
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 void	prependSequenceToFirstExon(java.lang.String prepend)	Prepend first's exons sequence with a given one
java.lang.String	showTranscripts(Genome genome)	Show a genome in a 'standard' way

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

debug

protected boolean debug

verbose

protected boolean verbose

randSeed

protected int randSeed

genomeName

protected java.lang.String 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

protected java.util.Random rand

config

protected Config config

genome

protected Genome genome

chromosome

protected Chromosome chromosome

gene

protected Gene gene

transcript

protected Transcript transcript

snpEffectPredictor

protected SnpEffectPredictor snpEffectPredictor

chromoSequence

protected java.lang.String chromoSequence

chromoBases

protected char[] chromoBases

codonTable

protected CodonTable codonTable

Constructor Detail

TestCasesBase

public TestCasesBase()

Method Detail

after

public void after()

before

public void before()

checkApply

public void checkApply(Variant variant,
                       Variant.VariantType varType,
                       java.lang.String expectedCds,
                       java.lang.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

public void checkApplyDel(Variant variant,
                          java.lang.String expectedCds,
                          java.lang.String expectedProtein,
                          int exonRank,
                          int expectedExon1Start,
                          int expectedExon1End)

checkApplyIns

public void checkApplyIns(Variant variant,
                          java.lang.String expectedCds,
                          java.lang.String expectedProtein,
                          int exonRank,
                          int expectedExon1Start,
                          int expectedExon1End)

checkApplyMixed

public void checkApplyMixed(Variant variant,
                            java.lang.String expectedCds,
                            java.lang.String expectedProtein,
                            int exonRank,
                            int expectedExon1Start,
                            int expectedExon1End)

checkApplyMnp

public void checkApplyMnp(Variant variant,
                          java.lang.String expectedCds,
                          java.lang.String expectedProtein,
                          int exonRank,
                          int expectedExon1Start,
                          int expectedExon1End)

checkApplySnp

public void checkApplySnp(Variant variant,
                          java.lang.String expectedCds,
                          java.lang.String expectedProtein,
                          int exonRank,
                          int expectedExon1Start,
                          int expectedExon1End)

checkEffect

protected void checkEffect(Variant variant,
                           EffectType effectExpected)

checkEffect

protected void checkEffect(Variant variant,
                           EffectType effectExpected,
                           EffectType effectNotExpected,
                           VariantEffect.EffectImpact impact)

formatVersion

protected EffFormatVersion formatVersion(java.lang.String vcfFileName)

Get file's format version

hasEffect

protected boolean hasEffect(java.lang.String effectExpected,
                            java.lang.String effStr)

Is effectExpected included in effStr (many effects delimited by '&'

init

protected void init()

initRand

protected void initRand()

initSnpEffPredictor

protected void initSnpEffPredictor()

initSnpEffPredictor

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?

prependSequenceToFirstExon

protected void prependSequenceToFirstExon(java.lang.String prepend)

Prepend first's exons sequence with a given one

showTranscripts

public java.lang.String showTranscripts(Genome genome)

Show a genome in a 'standard' way