Added unit tests for the SnpEff codec, and made minor adjustments to the codec itself.
This commit is contained in:
David Roazen
parent
dd974040af
commit
5e288136e0
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@ -80,6 +80,7 @@ public class SnpEffCodec implements FeatureCodec {
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}
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}
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try {
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try {
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trimAllFields(tokens);
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checkForRequiredFields(tokens, line);
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checkForRequiredFields(tokens, line);
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String contig = tokens[0];
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String contig = tokens[0];
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@ -126,6 +127,12 @@ public class SnpEffCodec implements FeatureCodec {
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}
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}
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}
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}
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private void trimAllFields ( String[] tokens ) {
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for ( int i = 0; i < tokens.length; i++ ) {
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tokens[i] = tokens[i].trim();
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}
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}
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private void checkForRequiredFields ( String[] tokens, String line ) {
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private void checkForRequiredFields ( String[] tokens, String line ) {
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for ( int requiredFieldIndex : REQUIRED_FIELDS ) {
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for ( int requiredFieldIndex : REQUIRED_FIELDS ) {
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if ( tokens[requiredFieldIndex].isEmpty() ) {
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if ( tokens[requiredFieldIndex].isEmpty() ) {
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@ -155,7 +162,7 @@ public class SnpEffCodec implements FeatureCodec {
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private String parseEffectExtraInformation ( String[] effectFieldTokens, boolean isNonCodingGene ) {
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private String parseEffectExtraInformation ( String[] effectFieldTokens, boolean isNonCodingGene ) {
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if ( (effectFieldTokens.length == 2 && ! isNonCodingGene) || effectFieldTokens.length == 3 ) {
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if ( (effectFieldTokens.length == 2 && ! isNonCodingGene) || effectFieldTokens.length == 3 ) {
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return effectFieldTokens[effectFieldTokens.length - 1];
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return effectFieldTokens[effectFieldTokens.length - 1].trim();
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}
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}
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return null;
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return null;
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@ -314,4 +314,67 @@ public class SnpEffFeature implements Feature {
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public String getCustomIntervalID() {
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public String getCustomIntervalID() {
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return customIntervalID;
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return customIntervalID;
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}
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}
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public boolean equals ( Object o ) {
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if ( o == null || ! (o instanceof SnpEffFeature) ) {
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return false;
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}
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SnpEffFeature other = (SnpEffFeature)o;
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return contig.equals(other.contig) &&
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position == other.position &&
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(reference == null ? other.reference == null : reference.equals(other.reference)) &&
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(change == null ? other.change == null : change.equals(other.change)) &&
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changeType == other.changeType &&
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zygosity == other.zygosity &&
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(quality == null ? other.quality == null : quality.equals(other.quality)) &&
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(coverage == null ? other.coverage == null : coverage.equals(other.coverage)) &&
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(warnings == null ? other.warnings == null : warnings.equals(other.warnings)) &&
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(geneID == null ? other.geneID == null : geneID.equals(other.geneID)) &&
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(geneName == null ? other.geneName == null : geneName.equals(other.geneName)) &&
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(bioType == null ? other.bioType == null : bioType.equals(other.bioType)) &&
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(transcriptID == null ? other.transcriptID == null : transcriptID.equals(other.transcriptID)) &&
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(exonID == null ? other.exonID == null : exonID.equals(other.exonID)) &&
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(exonRank == null ? other.exonRank == null : exonRank.equals(other.exonRank)) &&
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isNonCodingGene == other.isNonCodingGene &&
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effect == other.effect &&
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(effectExtraInformation == null ? other.effectExtraInformation == null : effectExtraInformation.equals(other.effectExtraInformation)) &&
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(oldAndNewAA == null ? other.oldAndNewAA == null : oldAndNewAA.equals(other.oldAndNewAA)) &&
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(oldAndNewCodon == null ? other.oldAndNewCodon == null : oldAndNewCodon.equals(other.oldAndNewCodon)) &&
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(codonNum == null ? other.codonNum == null : codonNum.equals(other.codonNum)) &&
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(cdsSize == null ? other.cdsSize == null : cdsSize.equals(other.cdsSize)) &&
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(codonsAround == null ? other.codonsAround == null : codonsAround.equals(other.codonsAround)) &&
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(aasAround == null ? other.aasAround == null : aasAround.equals(other.aasAround)) &&
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(customIntervalID == null ? other.customIntervalID == null : customIntervalID.equals(other.customIntervalID));
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}
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public String toString() {
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return "[Contig: " + contig +
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" Position: " + position +
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" Reference: " + reference +
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" Change: " + change +
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" Change Type: " + changeType +
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" Zygosity: " + zygosity +
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" Quality: " + quality +
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" Coverage: " + coverage +
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" Warnings: " + warnings +
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" Gene ID: " + geneID +
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" Gene Name: " + geneName +
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" Bio Type: " + bioType +
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" Transcript ID: " + transcriptID +
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" Exon ID: " + exonID +
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" Exon Rank: " + exonRank +
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" Non-Coding Gene: " + isNonCodingGene +
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" Effect: " + effect +
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" Effect Extra Information: " + effectExtraInformation +
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" Old/New AA: " + oldAndNewAA +
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" Old/New Codon: " + oldAndNewCodon +
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" Codon Num: " + codonNum +
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" CDS Size: " + cdsSize +
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" Codons Around: " + codonsAround +
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" AAs Around: " + aasAround +
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" Custom Interval ID: " + customIntervalID +
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"]";
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}
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}
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}
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@ -0,0 +1,259 @@
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils.codecs.snpEff;
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import org.apache.commons.io.input.ReaderInputStream;
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import org.broad.tribble.TribbleException;
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import org.broad.tribble.readers.AsciiLineReader;
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import org.broad.tribble.readers.LineReader;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.EffectType;
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import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.ChangeType;
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import static org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants.Zygosity;
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import java.io.StringReader;
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public class SnpEffCodecUnitTest {
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@Test
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public void testParseWellFormedSnpEffHeaderLine() {
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String wellFormedSnpEffHeaderLine = "# Chromo\tPosition\tReference\tChange\tChange type\t" +
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"Homozygous\tQuality\tCoverage\tWarnings\tGene_ID\tGene_name\tBio_type\tTrancript_ID\tExon_ID\t" +
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"Exon_Rank\tEffect\told_AA/new_AA\tOld_codon/New_codon\tCodon_Num(CDS)\tCDS_size\tCodons around\t" +
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"AAs around\tCustom_interval_ID";
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SnpEffCodec codec = new SnpEffCodec();
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LineReader reader = new AsciiLineReader(new ReaderInputStream(new StringReader(wellFormedSnpEffHeaderLine)));
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String headerReturned = (String)codec.readHeader(reader);
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Assert.assertEquals(headerReturned, wellFormedSnpEffHeaderLine);
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}
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@Test(expectedExceptions = TribbleException.InvalidHeader.class)
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public void testParseWrongNumberOfFieldsSnpEffHeaderLine() {
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String wrongNumberOfFieldsSnpEffHeaderLine = "# Chromo\tPosition\tReference\tChange\tChange type\t" +
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"Homozygous\tQuality\tCoverage\tWarnings\tGene_ID\tGene_name\tBio_type\tTrancript_ID\tExon_ID\t" +
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"Exon_Rank\tEffect\told_AA/new_AA\tOld_codon/New_codon\tCodon_Num(CDS)\tCDS_size\tCodons around\t" +
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"AAs around";
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SnpEffCodec codec = new SnpEffCodec();
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LineReader reader = new AsciiLineReader(new ReaderInputStream(new StringReader(wrongNumberOfFieldsSnpEffHeaderLine)));
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codec.readHeader(reader);
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}
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@Test(expectedExceptions = TribbleException.InvalidHeader.class)
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public void testParseMisnamedColumnSnpEffHeaderLine() {
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String misnamedColumnSnpEffHeaderLine = "# Chromo\tPosition\tRef\tChange\tChange type\t" +
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"Homozygous\tQuality\tCoverage\tWarnings\tGene_ID\tGene_name\tBio_type\tTrancript_ID\tExon_ID\t" +
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"Exon_Rank\tEffect\told_AA/new_AA\tOld_codon/New_codon\tCodon_Num(CDS)\tCDS_size\tCodons around\t" +
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"AAs around\tCustom_interval_ID";
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SnpEffCodec codec = new SnpEffCodec();
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LineReader reader = new AsciiLineReader(new ReaderInputStream(new StringReader(misnamedColumnSnpEffHeaderLine)));
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codec.readHeader(reader);
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}
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@Test
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public void testParseSimpleEffectSnpEffLine() {
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String simpleEffectSnpEffLine = "1\t69428\tT\tG\tSNP\tHom\t6049.69\t61573\t\tENSG00000177693\t" +
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"OR4F5\tmRNA\tENST00000326183\texon_1_69055_70108\t1\tNON_SYNONYMOUS_CODING\tF/C\tTTT/TGT\t113\t918\t\t\t";
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SnpEffFeature expectedFeature = new SnpEffFeature("1",
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69428l,
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"T",
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"G",
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ChangeType.SNP,
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Zygosity.Hom,
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6049.69,
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61573l,
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null,
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"ENSG00000177693",
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"OR4F5",
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"mRNA",
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"ENST00000326183",
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"exon_1_69055_70108",
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1,
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false,
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EffectType.NON_SYNONYMOUS_CODING,
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null,
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"F/C",
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"TTT/TGT",
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113,
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918,
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null,
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null,
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null
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);
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SnpEffCodec codec = new SnpEffCodec();
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SnpEffFeature feature = (SnpEffFeature)codec.decode(simpleEffectSnpEffLine);
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Assert.assertEquals(feature, expectedFeature);
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}
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@Test
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public void testParseNonCodingRegionSnpEffLine() {
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String nonCodingRegionSnpEffLine = "1\t1337592\tG\tC\tSNP\tHom\t1935.52\t21885\t\tENSG00000250188\t" +
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"RP4-758J18.5\tmRNA\tENST00000514958\texon_1_1337454_1338076\t2\tWITHIN_NON_CODING_GENE, NON_SYNONYMOUS_CODING\t" +
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"L/V\tCTA/GTA\t272\t952\t\t\t";
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SnpEffFeature expectedFeature = new SnpEffFeature("1",
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1337592l,
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"G",
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"C",
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ChangeType.SNP,
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Zygosity.Hom,
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1935.52,
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21885l,
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null,
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"ENSG00000250188",
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"RP4-758J18.5",
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"mRNA",
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"ENST00000514958",
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"exon_1_1337454_1338076",
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2,
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true,
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EffectType.NON_SYNONYMOUS_CODING,
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null,
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"L/V",
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"CTA/GTA",
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272,
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952,
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null,
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null,
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null
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);
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SnpEffCodec codec = new SnpEffCodec();
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SnpEffFeature feature = (SnpEffFeature)codec.decode(nonCodingRegionSnpEffLine);
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Assert.assertEquals(feature, expectedFeature);
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}
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@Test
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public void testParseExtraEffectInformationSnpEffLine() {
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String extraEffectInformationSnpEffLine = "1\t879537\tT\tC\tSNP\tHom\t341.58\t13733\t\tENSG00000187634\tSAMD11\t" +
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"mRNA\tENST00000341065\t\t\tUTR_3_PRIME: 4 bases from transcript end\t\t\t\t\t\t\t";
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SnpEffFeature expectedFeature = new SnpEffFeature("1",
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879537l,
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"T",
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"C",
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ChangeType.SNP,
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Zygosity.Hom,
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341.58,
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13733l,
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null,
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"ENSG00000187634",
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"SAMD11",
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"mRNA",
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"ENST00000341065",
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null,
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null,
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false,
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EffectType.UTR_3_PRIME,
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"4 bases from transcript end",
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null,
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null,
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null,
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null,
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null,
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null,
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null
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);
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SnpEffCodec codec = new SnpEffCodec();
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SnpEffFeature feature = (SnpEffFeature)codec.decode(extraEffectInformationSnpEffLine);
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Assert.assertEquals(feature, expectedFeature);
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}
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@Test
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public void testParseMultiEffectSnpEffLine() {
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String multiEffectSnpEffLine = "1\t901901\tC\tT\tSNP\tHom\t162.91\t4646\t\tENSG00000187583\tPLEKHN1\tmRNA\t" +
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"ENST00000379410\texon_1_901877_901994\t1\tSTART_GAINED: ATG, UTR_5_PRIME: 11 bases from TSS\t\t\t\t\t\t\t";
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SnpEffFeature expectedFeature = new SnpEffFeature("1",
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901901l,
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"C",
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"T",
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ChangeType.SNP,
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Zygosity.Hom,
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162.91,
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4646l,
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null,
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"ENSG00000187583",
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"PLEKHN1",
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"mRNA",
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"ENST00000379410",
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"exon_1_901877_901994",
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1,
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false,
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EffectType.START_GAINED,
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"ATG, UTR_5_PRIME: 11 bases from TSS",
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null,
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null,
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null,
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null,
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null,
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null,
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null
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);
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SnpEffCodec codec = new SnpEffCodec();
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SnpEffFeature feature = (SnpEffFeature)codec.decode(multiEffectSnpEffLine);
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Assert.assertEquals(feature, expectedFeature);
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}
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@Test(expectedExceptions = TribbleException.InvalidDecodeLine.class)
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public void testParseWrongNumberOfFieldsSnpEffLine() {
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String wrongNumberOfFieldsSnpEffLine = "1\t69428\tT\tG\tSNP\tHom\t6049.69\t61573\t\tENSG00000177693\t" +
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||||||
|
"OR4F5\tmRNA\tENST00000326183\texon_1_69055_70108\t1\tNON_SYNONYMOUS_CODING\tF/C\tTTT/TGT\t113\t918\t\t";
|
||||||
|
|
||||||
|
SnpEffCodec codec = new SnpEffCodec();
|
||||||
|
SnpEffFeature feature = (SnpEffFeature)codec.decode(wrongNumberOfFieldsSnpEffLine);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test(expectedExceptions = TribbleException.InvalidDecodeLine.class)
|
||||||
|
public void testParseBlankEffectFieldSnpEffLine() {
|
||||||
|
String blankEffectFieldSnpEffLine = "1\t69428\tT\tG\tSNP\tHom\t6049.69\t61573\t\tENSG00000177693\t" +
|
||||||
|
"OR4F5\tmRNA\tENST00000326183\texon_1_69055_70108\t1\t\tF/C\tTTT/TGT\t113\t918\t\t\t";
|
||||||
|
|
||||||
|
SnpEffCodec codec = new SnpEffCodec();
|
||||||
|
SnpEffFeature feature = (SnpEffFeature)codec.decode(blankEffectFieldSnpEffLine);
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test(expectedExceptions = TribbleException.InvalidDecodeLine.class)
|
||||||
|
public void testParseInvalidNumericFieldSnpEffLine() {
|
||||||
|
String invalidNumericFieldSnpEffLine = "1\t69428\tT\tG\tSNP\tHom\t6049.69\t61573\t\tENSG00000177693\t" +
|
||||||
|
"OR4F5\tmRNA\tENST00000326183\texon_1_69055_70108\t1\tNON_SYNONYMOUS_CODING\tF/C\tTTT/TGT\t113\tfoo\t\t\t";;
|
||||||
|
|
||||||
|
SnpEffCodec codec = new SnpEffCodec();
|
||||||
|
SnpEffFeature feature = (SnpEffFeature)codec.decode(invalidNumericFieldSnpEffLine);
|
||||||
|
}
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue