Package org.broadinstitute.gatk.tools.walkers.annotator.SnpEff

Examples of org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.SnpEffEffect

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    @Test
    public void testParseWellFormedEffect() {
        String effectName = "NON_SYNONYMOUS_CODING";
        String[] effectMetadata = { "MODERATE", "MISSENSE", "Aca/Gca", "T/A", "OR4F5", "protein_coding", "CODING", "ENST00000534990", "exon_1_69037_69829" };

        SnpEffEffect effect = new SnpEffEffect(effectName, effectMetadata);
        Assert.assertTrue( effect.isWellFormed() && effect.isCoding() );
    }
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    @Test
    public void testParseInvalidEffectNameEffect() {
        String effectName = "MADE_UP_EFFECT";
        String[] effectMetadata = { "MODERATE", "MISSENSE", "Aca/Gca", "T/A", "OR4F5", "protein_coding", "CODING", "ENST00000534990", "exon_1_69037_69829" };

        SnpEffEffect effect = new SnpEffEffect(effectName, effectMetadata);
        Assert.assertFalse(effect.isWellFormed());
    }
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    @Test
    public void testParseInvalidEffectImpactEffect() {
        String effectName = "NON_SYNONYMOUS_CODING";
        String[] effectMetadata = { "MEDIUM", "MISSENSE", "Aca/Gca", "T/A", "OR4F5", "protein_coding", "CODING", "ENST00000534990", "exon_1_69037_69829" };

        SnpEffEffect effect = new SnpEffEffect(effectName, effectMetadata);
        Assert.assertFalse(effect.isWellFormed());
    }
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    @Test
    public void testParseWrongNumberOfMetadataFieldsEffect() {
        String effectName = "NON_SYNONYMOUS_CODING";
        String[] effectMetadata = { "MODERATE", "MISSENSE", "Aca/Gca", "T/A", "OR4F5", "protein_coding", "CODING", "ENST00000534990" };

        SnpEffEffect effect = new SnpEffEffect(effectName, effectMetadata);
        Assert.assertFalse(effect.isWellFormed());
    }
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    @Test
    public void testParseSnpEffOneWarningOrErrorEffect() {
        String effectName = "NON_SYNONYMOUS_CODING";
        String[] effectMetadata = { "MODERATE", "MISSENSE", "Aca/Gca", "T/A", "OR4F5", "protein_coding", "CODING", "ENST00000534990", "exon_1_69037_69829", "SNPEFF_WARNING_OR_ERROR_TEXT" };

        SnpEffEffect effect = new SnpEffEffect(effectName, effectMetadata);
        Assert.assertTrue( ! effect.isWellFormed() && effect.getParseError().equals("SnpEff issued the following warning or error: \"SNPEFF_WARNING_OR_ERROR_TEXT\"") );
    }
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    @Test
    public void testParseSnpEffBothWarningAndErrorEffect() {
        String effectName = "NON_SYNONYMOUS_CODING";
        String[] effectMetadata = { "MODERATE", "MISSENSE", "Aca/Gca", "T/A", "OR4F5", "protein_coding", "CODING", "ENST00000534990", "exon_1_69037_69829", "SNPEFF_WARNING_TEXT", "SNPEFF_ERROR_TEXT" };

        SnpEffEffect effect = new SnpEffEffect(effectName, effectMetadata);
        Assert.assertTrue( ! effect.isWellFormed() && effect.getParseError().equals("SnpEff issued the following warning: \"SNPEFF_WARNING_TEXT\", and the following error: \"SNPEFF_ERROR_TEXT\"") );
    }
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Related Classes of org.broadinstitute.gatk.tools.walkers.annotator.SnpEff.SnpEffEffect

  • org.broadinstitute.gatk.tools.walkers.annotator.SnpEffUnitTest
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