Class TestCasesStructuralTranslocations


  • public class TestCasesStructuralTranslocations
    extends java.lang.Object
    Test case for structural variants: Translocation (fusions)

    We create two genes (one transcript each). Each gene is in one different chromosome

    Transcripts: 1:10-90, strand: +, id:tr1, Protein Exons: 1:10-30 'exon1', rank: 1, frame: ., sequence: tatttgtatgaggatttgagt 1:40-90 'exon2', rank: 2, frame: ., sequence: tactcagtgctgggcaatcccttagctgtcgcgccgcttaccctactattc CDS : tatttgtatgaggatttgagttactcagtgctgggcaatcccttagctgtcgcgccgcttaccctactattc Protein : YLYEDLSYSVLGNPLAVAPLTLLF

    2:110-190, strand: +, id:tr2, Protein Exons: 2:110-125 'exon3', rank: 1, frame: ., sequence: gttaatgggatttcac 2:150-190 'exon4', rank: 2, frame: ., sequence: atgggaacggagtgtcgacagcaccttatggggagctatat CDS : gttaatgggatttcacatgggaacggagtgtcgacagcaccttatggggagctatat Protein : VNGISHGNGVSTAPYGELY

    Genes diagram:

    [ Chr1: Gene1 ] >>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | | | | ^10 ^30 ^40 ^90

    [ Chr2: Gene2 ] >>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | | | | ^110 ^125 ^150 ^190

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected void checkEffects​(Variant variant, EffectType[] expEffs, EffectType[] notExpEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact)  
      void init​(boolean gene1NegativeStrand, boolean gene2NegativeStrand)  
      void test01_0()
      Translocation in the same direction (both genes in positive strand)
      void test01_0_nonFs()
      Translocation in the same direction (both genes in positive strand)
      void test01_1()
      Translocation in opposite directions
      void test01_2()
      Translocation in opposite directions
      void test01_3()
      Translocation in the same direction (both genes in negative strand)
      void test01_3_noFs()
      Translocation in the same direction (both genes in negative strand)
      void test02_0()
      Translocation in opposite directions (both genes in positive strand)
      void test02_1()
      Translocation in the same direction
      void test02_1_nonFs()
      Translocation in the same direction
      void test02_2()
      Translocation in the same direction
      void test02_2_nonFs()
      Translocation in the same direction
      void test02_3()
      Translocation in the opposite directions
      void test03_0()
      Translocation in opposite directions
      void test03_1()
      Translocation in the same direction
      void test03_1_nonFs()
      Translocation in the same direction
      void test03_2()
      Translocation in the same direction
      void test03_2_nonFs()
      Translocation in the same direction
      void test03_3()
      Translocation in the opposite directions
      void test04_0()
      Translocation in the same direction (both genes in positive strand)
      void test04_0_nonFs()
      Translocation in the same direction (both genes in positive strand)
      void test04_1()
      Translocation in opposite directions
      void test04_2()
      Translocation in opposite directions
      void test04_3()
      Translocation in the same direction
      void test04_3_nonFs()
      Translocation in the same direction
      void test05_1_one_gene()
      Translocation affecting a gene and an intergenic region
      void test05_2_one_gene()
      Translocation affecting a gene and an intergenic region
      void test06_no_gene()
      Translocation not affecting any gene (intergenic regions)
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • TestCasesStructuralTranslocations

        public TestCasesStructuralTranslocations()
    • Method Detail

      • init

        public void init​(boolean gene1NegativeStrand,
                         boolean gene2NegativeStrand)
      • test01_0

        @Test
        public void test01_0()
        Translocation in the same direction (both genes in positive strand)

        #CHROM POS ID REF ALT chr1 35 . N N[chr2:140[

        gene1: >>>>>>>>>>>---- | gene2 ---->>>>>>>>>

      • test01_0_nonFs

        @Test
        public void test01_0_nonFs()
        Translocation in the same direction (both genes in positive strand)

        #CHROM POS ID REF ALT chr1 35 . N N[chr2:140[

        gene1: >>>>>>>>>>>---- | gene2 ---->>>>>>>>>>>>---

      • test01_1

        @Test
        public void test01_1()
        Translocation in opposite directions

        #CHROM POS ID REF ALT chr1 35 . N N[chr2:140[

        gene1: >>>>>>>>>>>---- | gene2 ----<<<<<<<<<<<<---

      • test01_2

        @Test
        public void test01_2()
        Translocation in opposite directions

        #CHROM POS ID REF ALT chr1 35 . N N[chr2:140[

        gene1: <<<<<<<<<<<<---- | gene2 ---->>>>>>>>>----

      • test01_3

        @Test
        public void test01_3()
        Translocation in the same direction (both genes in negative strand)

        #CHROM POS ID REF ALT chr1 35 . N N[chr2:140[

        gene1: <<<<<<<<<<<<---- | gene2 ----<<<<<<<<<<<<---

      • test01_3_noFs

        @Test
        public void test01_3_noFs()
        Translocation in the same direction (both genes in negative strand)

        #CHROM POS ID REF ALT chr1 35 . N N[chr2:140[

        gene1: <<<<<<<<<<<<---- | gene2 --<<<<<<<<<<<<---

      • test02_0

        @Test
        public void test02_0()
        Translocation in opposite directions (both genes in positive strand)

        #CHROM POS ID REF ALT chr1 35 . N N]chr2:140]

        gene1: >>>>>>>>>>>---- | gene2 >>>>>>>>>>>----

      • test02_1

        @Test
        public void test02_1()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N N]chr2:140]

        gene1: >>>>>>>>>>>---- | gene2 <<<<<<<<<<<----

      • test02_1_nonFs

        @Test
        public void test02_1_nonFs()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N N]chr2:140]

        gene1: >>>>>>>>>>>---- | gene2 -----<<<<<<<<<<<----

      • test02_2

        @Test
        public void test02_2()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N N]chr2:140]

        gene1: <<<<<<<<<<<---- | gene2 >>>>>>>>>>>----

      • test02_2_nonFs

        @Test
        public void test02_2_nonFs()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N N]chr2:140]

        gene1: <<<<<<<<<<<---- | gene2 ----->>>>>>>>>>>----

      • test02_3

        @Test
        public void test02_3()
        Translocation in the opposite directions

        #CHROM POS ID REF ALT chr1 35 . N N]chr2:140]

        gene1: <<<<<<<<<<<---- | gene2 <<<<<<<<<<<----

      • test03_0

        @Test
        public void test03_0()
        Translocation in opposite directions

        #CHROM POS ID REF ALT chr1 35 . N [chr2:140[N

        gene1: --->>>>>>>>>>>---- | gene2 --->>>>>>>>>>>----

      • test03_1

        @Test
        public void test03_1()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N [chr2:140[N

        gene1: --->>>>>>>>>>>---- | gene2 ---<<<<<<<<<<----

      • test03_1_nonFs

        @Test
        public void test03_1_nonFs()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N [chr2:140[N

        gene1: --->>>>>>>>>>>---- | gene2 ---<<<<<<<<<<----

      • test03_2

        @Test
        public void test03_2()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N [chr2:140[N

        gene1: ---<<<<<<<<<<<---- | gene2 --->>>>>>>>>>>----

      • test03_2_nonFs

        @Test
        public void test03_2_nonFs()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N [chr2:140[N

        gene1: ---<<<<<<<<<<<---- | gene2 >>>>>>>>>>>----

      • test03_3

        @Test
        public void test03_3()
        Translocation in the opposite directions

        #CHROM POS ID REF ALT chr1 35 . N [chr2:140[N

        gene1: ---<<<<<<<<<<<---- | gene2 ---<<<<<<<<<<<----

      • test04_0

        @Test
        public void test04_0()
        Translocation in the same direction (both genes in positive strand)

        #CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N

        gene1: --->>>>>>>>>>>---- | gene2 --->>>>>>>>>>>----

      • test04_0_nonFs

        @Test
        public void test04_0_nonFs()
        Translocation in the same direction (both genes in positive strand)

        #CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N

        gene1: --->>>>>>>>>>>---- | gene2 --->>>>>>>>>>>

      • test04_1

        @Test
        public void test04_1()
        Translocation in opposite directions

        #CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N

        gene1: --->>>>>>>>>>>---- | gene2 ---<<<<<<<<<<<----

      • test04_2

        @Test
        public void test04_2()
        Translocation in opposite directions

        #CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N

        gene1: ---<<<<<<<<<<<<<<---- | gene2 --->>>>>>>>>>>----

      • test04_3

        @Test
        public void test04_3()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N

        gene1: ---<<<<<<<<<<<<---- | gene2 ---<<<<<<<<<<<----

      • test04_3_nonFs

        @Test
        public void test04_3_nonFs()
        Translocation in the same direction

        #CHROM POS ID REF ALT chr1 35 . N ]chr2:140]N

        gene1: ---<<<<<<<<<<<<---- | gene2 ---<<<<<<<<<<<----

      • test05_1_one_gene

        @Test
        public void test05_1_one_gene()
        Translocation affecting a gene and an intergenic region

        [ Chr1: Gene1 ] ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.............................................................................................................. ^10 ^30 | ^40 ^90 | |> ------------------ <| | | ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......... ^110 ^125 ^150 ^190 [ Chr2: Gene2 ]

      • test05_2_one_gene

        @Test
        public void test05_2_one_gene()
        Translocation affecting a gene and an intergenic region

        [ Chr1: Gene1 ] ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.............................................................................................................. ^10 ^30 ^40 ^90 | |> ------------ <| | ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......... ^110 ^125 ^150 ^190 [ Chr2: Gene2 ]

      • test06_no_gene

        @Test
        public void test06_no_gene()
        Translocation not affecting any gene (intergenic regions)

        [ Chr1: Gene1 ] ......>>>>>>>>>>>>>>>>>>>>>--------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.............................................................................................................. ^10 ^30 ^40 ^90 | <|------------------------------------------------------------------------------------|> | ..........................................................................................................>>>>>>>>>>>>>>>>------------------------>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>.......... ^110 ^125 ^150 ^190 [ Chr2: Gene2 ]