Class TestGenome


  • public class TestGenome
    extends java.lang.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 Detail

      • strandMinus

        public boolean strandMinus
      • verbose

        public boolean verbose
      • config

        public Config config
      • genomeName

        public java.lang.String genomeName
      • genome

        public Genome genome
      • gene

        public Gene gene
    • Constructor Detail

      • TestGenome

        public TestGenome​(boolean strandMinus)
    • Method Detail

      • 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