org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply Maven / Gradle / Ivy
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Variant annotation and effect prediction package.
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package org.snpeff.snpEffect.testCases.unity;
import org.snpeff.interval.BioType;
import org.snpeff.interval.Chromosome;
import org.snpeff.interval.Exon;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Transcript;
import org.snpeff.snpEffect.Config;
import org.snpeff.snpEffect.SnpEffectPredictor;
/**
* Test case
*
* Transcript:
* 1:0-999, strand: +, id:transcript1, Protein
* Exons:
* 1:100-199 'exon1', rank: 1, frame: ., sequence: atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg
* 1:300-399 'exon2', rank: 2, frame: ., sequence: tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg
* 1:900-999 'exon3', rank: 0, frame: ., sequence: ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg
* CDS : atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatggtgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacgggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg
* Protein : MSAGEGIHAARILMLPRWILSEIWCPGREGHIMVFGNSRARFCSKLNWQLGINPDPIVTHGSIHPQRVEEKHLTPIEQDLFRNTLYRLPIYLIPHIYFIG
*
*
* Transcript (full coordinates):
* 0
* 0 1 2 3 4 5 6 7 8 9
* 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9
* 0123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
* ....................................................................................................atgtccgcaggtgaaggcatacacgctgcgcgtatactgatgttacctcgatggattttgtcagaaatatggtgcccaggacgcgaagggcatattatgg....................................................................................................tgtttgggaattcacgggcacggttctgcagcaagctgaattggcagctcggcataaatcccgaccccatcgtcacgcacggatcaattcatcctcaacg....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ggtagaggaaaagcacctaacccccattgagcaggatctctttcgtaatactctgtatcgattaccgatttatttgattccccacatttatttcatcggg
* M S A G E G I H A A R I L M L P R W I L S E I W C P G R E G H I M V F G N S R A R F C S K L N W Q L G I N P D P I V T H G S I H P Q R V E E K H L T P I E Q D L F R N T L Y R L P I Y L I P H I Y F I G
* 0120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120120 1201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201201 2012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012012
* ---------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>---------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
* | | | | | |
* | | | | | |^999
* | | | | |^900
* | | | |^399
* | | |^300
* | |^199
* |^100
*/
public class TestCasesBaseApply extends TestCasesBase {
public TestCasesBaseApply() {
super();
}
@Override
protected void initSnpEffPredictor() {
// Create a config and force out snpPredictor
if (config == null || config.getGenome() == null || !config.getGenome().getGenomeName().equals(genomeName)) {
config = new Config(genomeName, Config.DEFAULT_CONFIG_FILE);
}
// Create predictor
genome = config.getGenome();
snpEffectPredictor = new SnpEffectPredictor(genome);
// Chromosome sequence
chromosome = new Chromosome(genome, 0, 1000, "1");
chromoSequence = "ATTGGCTCGACGCTCATTCACTCCAACAGCCCGGGACCCCCGCTCAATTATTTCACTCACCGGGAAAATTGTACCGATTGTCCGTGCCTTACTTCAAATGATGTCCGCAGGTGAAGGCATACACGCTGCGCGTATACTGATGTTACCTCGATGGATTTTGTCAGAAATATGGTGCCCAGGACGCGAAGGGCATATTATGGTTGCGCGAAGACATCATTTTGGAACTAACTACTAGAACTAATCAGTAAACATCCTACTGGACGGCTTGCCCCGCGATTCAAACCGCTAACTTTATCGTCCTGTTTGGGAATTCACGGGCACGGTTCTGCAGCAAGCTGAATTGGCAGCTCGGCATAAATCCCGACCCCATCGTCACGCACGGATCAATTCATCCTCAACGAAAGGGAGCTAGCGCTGTACGGCCACGGGAGGGTGTGCACCATATTCAACGACTTCTTAACCCGACCTTAAACCAATCTTCTTACGAATGTGCCGTCGAGCGGCACCTTTCAGATTTCAGTGTTGCAACTCTTACCAGTGCACTTAAACACTCCCTCAAATCACAGGCCTTGTTCTATAGCGCTCAGCACGTCGCCAGGATGCTGGTACGCCGGACTGTCCAGATACCGTTAGCACGGCATAGGGAGGATCGCGCAGGCTATACCCGATATCGGTTGGGCATCCTTTAATTCTTTGCGGATGCGAATACCCGTCACCCCTTGCGATTCTGTTTAACGCAGACTCAACCTAACGATTGACCTACATAGTAATGAGTTTTGTTGGTCCGTAAGACTTCGCCCAAAACCGCGCATGGTGGTCGTAGAAACGTACTCACAGGCCACTAAATCCGCTTAGGACATACAGTCTCCTTCGGTCACATTAACCCCATATGATTAGTACGGTAGAGGAAAAGCACCTAACCCCCATTGAGCAGGATCTCTTTCGTAATACTCTGTATCGATTACCGATTTATTTGATTCCCCACATTTATTTCATCGGG"; // A";
chromoBases = chromoSequence.toCharArray();
codonTable = genome.codonTable();
// Create gene, trancript and exons
gene = new Gene(chromosome, 0, 999, false, "gene1", "gene1", BioType.protein_coding);
transcript = new Transcript(gene, gene.getStart(), gene.getEnd(), gene.isStrandMinus(), "transcript1");
transcript.setProteinCoding(true);
Exon exons[] = new Exon[3];
exons[0] = new Exon(transcript, 100, 199, false, "exon1", 0);
exons[1] = new Exon(transcript, 300, 399, false, "exon2", 0);
exons[2] = new Exon(transcript, 900, 999, false, "exon3", 0);
for (Exon ex : exons) {
ex.setSequence(chromoSequence.substring(ex.getStart(), ex.getEnd() + 1));
transcript.add(ex);
}
// Create genomic sequences
genome.getGenomicSequences().addGeneSequences(chromosome.getId(), chromoSequence);
// Set predictor parameters
snpEffectPredictor.setSpliceRegionExonSize(spliceRegionExonSize);
snpEffectPredictor.setSpliceRegionIntronMin(spliceRegionIntronMin);
snpEffectPredictor.setSpliceRegionIntronMax(spliceRegionIntronMax);
snpEffectPredictor.setUpDownStreamLength(0);
// Update config
config.setSnpEffectPredictor(snpEffectPredictor);
config.setHgvsShift(shiftHgvs);
// Build forest
snpEffectPredictor.buildForest();
}
}
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