Class TestGenome

java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestGenome

public class TestGenome extends Object
Creates a simple "genome" for testing:

Forward strand: 1:1000-2000, strand: +, id:tr1, Protein Exons: 1:1000-1049 'exon1000', rank: 0, frame: ., sequence: tcccccccatcatagcctgaaggccccatgaataagcgtagaagacatgc 1:1100-1149 'exon1100', rank: 1, frame: ., sequence: ggctcatatgtatcgttttcgtggcttcgtacgtccgcgagtatccattg 1:1200-1249 'exon1200', rank: 2, frame: ., sequence: ctcctgaacttgtgtacctagaatacgtcggaaacaagcaatcaaccagc 1:1300-1349 'exon1300', rank: 3, frame: ., sequence: ctcccgtctccgcaggagttttcttcgtatctcacgcttctgctaatcta 1:1400-1449 'exon1400', rank: 4, frame: ., sequence: gtacggcgaatattgacaagaacggtggtatttattagaatttgcatatg 1:1500-1549 'exon1500', rank: 5, frame: ., sequence: ggtactaaagtcggaggcgggtaacgtaatcgccgcgggacgggttcagc 1:1600-1649 'exon1600', rank: 6, frame: ., sequence: tcgtaaacctaaagctataattttcacgacgctcgcaccgttcaaaaatc 1:1700-1749 'exon1700', rank: 7, frame: ., sequence: tatcgcgggttgcgtaagtttaggtatactcctggttctggattccacat 1:1800-1849 'exon1800', rank: 8, frame: ., sequence: cctaataaccagtggctccgatctggccttcttgcggcgaatttggagga 1:1900-1949 'exon1900', rank: 9, frame: ., sequence: cggctgcagcgtaaatatgtcgtttaccggggacagaaggacggaagcta CDS : tcccccccatcatagcctgaaggccccatgaataagcgtagaagacatgcggctcatatgtatcgttttcgtggcttcgtacgtccgcgagtatccattgctcctgaacttgtgtacctagaatacgtcggaaacaagcaatcaaccagcctcccgtctccgcaggagttttcttcgtatctcacgcttctgctaatctagtacggcgaatattgacaagaacggtggtatttattagaatttgcatatgggtactaaagtcggaggcgggtaacgtaatcgccgcgggacgggttcagctcgtaaacctaaagctataattttcacgacgctcgcaccgttcaaaaatctatcgcgggttgcgtaagtttaggtatactcctggttctggattccacatcctaataaccagtggctccgatctggccttcttgcggcgaatttggaggacggctgcagcgtaaatatgtcgtttaccggggacagaaggacggaagcta Protein : SPPS*PEGPMNKRRRHAAHMYRFRGFVRPRVSIAPELVYLEYVGNKQSTSLPSPQEFSSYLTLLLI*YGEY*QERWYLLEFAYGY*SRRRVT*SPRDGFSS*T*SYNFHDARTVQKSIAGCVSLGILLVLDSTS**PVAPIWPSCGEFGGRLQRKYVVYRGQKDGS?

Reverse strand: 1:1000-2000, strand: -, id:tr1, Protein Exons: 1:1000-1049 'exon1000', rank: 1000, frame: ., sequence: tcccccccatcatagcctgaaggccccatgaataagcgtagaagacatgc 1:1100-1149 'exon1100', rank: 1100, frame: ., sequence: ggctcatatgtatcgttttcgtggcttcgtacgtccgcgagtatccattg 1:1200-1249 'exon1200', rank: 1200, frame: ., sequence: ctcctgaacttgtgtacctagaatacgtcggaaacaagcaatcaaccagc 1:1300-1349 'exon1300', rank: 1300, frame: ., sequence: ctcccgtctccgcaggagttttcttcgtatctcacgcttctgctaatcta 1:1400-1449 'exon1400', rank: 1400, frame: ., sequence: gtacggcgaatattgacaagaacggtggtatttattagaatttgcatatg 1:1500-1549 'exon1500', rank: 1500, frame: ., sequence: ggtactaaagtcggaggcgggtaacgtaatcgccgcgggacgggttcagc 1:1600-1649 'exon1600', rank: 1600, frame: ., sequence: tcgtaaacctaaagctataattttcacgacgctcgcaccgttcaaaaatc 1:1700-1749 'exon1700', rank: 1700, frame: ., sequence: tatcgcgggttgcgtaagtttaggtatactcctggttctggattccacat 1:1800-1849 'exon1800', rank: 1800, frame: ., sequence: cctaataaccagtggctccgatctggccttcttgcggcgaatttggagga 1:1900-1949 'exon1900', rank: 1900, frame: ., sequence: cggctgcagcgtaaatatgtcgtttaccggggacagaaggacggaagcta CDS : cggctgcagcgtaaatatgtcgtttaccggggacagaaggacggaagctacctaataaccagtggctccgatctggccttcttgcggcgaatttggaggatatcgcgggttgcgtaagtttaggtatactcctggttctggattccacattcgtaaacctaaagctataattttcacgacgctcgcaccgttcaaaaatcggtactaaagtcggaggcgggtaacgtaatcgccgcgggacgggttcagcgtacggcgaatattgacaagaacggtggtatttattagaatttgcatatgctcccgtctccgcaggagttttcttcgtatctcacgcttctgctaatctactcctgaacttgtgtacctagaatacgtcggaaacaagcaatcaaccagcggctcatatgtatcgttttcgtggcttcgtacgtccgcgagtatccattgtcccccccatcatagcctgaaggccccatgaataagcgtagaagacatgc Protein : RLQRKYVVYRGQKDGSYLITSGSDLAFLRRIWRISRVA*V*VYSWFWIPHS*T*SYNFHDARTVQKSVLKSEAGNVIAAGRVQRTANIDKNGGIY*NLHMLPSPQEFSSYLTLLLIYS*TCVPRIRRKQAINQRLICIVFVASYVREYPLSPPS*PEGPMNKRRRH?

  • Field Details

    • strandMinus

      public boolean strandMinus
    • verbose

      public boolean verbose
    • config

      public Config config
    • genomeName

      public String genomeName
    • genome

      public Genome genome
    • chr

      public Chromosome chr
    • gene

      public Gene gene
    • tr

      public Transcript tr
    • snpEffectPredictor

      public SnpEffectPredictor snpEffectPredictor
    • markers

      public Markers markers
  • Constructor Details

    • TestGenome

      public TestGenome(boolean strandMinus)
  • Method Details

    • add

      public void add(Marker marker)
      Add markers to SnpEffPredictor
    • checkEffect

      public void checkEffect(Variant variant, EffectType effectTypeExpected, VariantEffect.EffectImpact effectImpactExpected, int countMatchExpected)
      Apply a predictor to a variant and check whether the expected number of matches are found
    • createSnpEffectPredictor

      public SnpEffectPredictor createSnpEffectPredictor()
      Create a snpEff predictor and build the forest