Package bgu.bio.adt.rna

Examples of bgu.bio.adt.rna.RNASpecificTree

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public class TestSizeRelatedCostCalculator {
  @Test
  public void testSimple1(){
    RNASpecificTree t = new RNASpecificTree();
    t.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
        "...((((...))...(((...)))..))....".toCharArray());
   
    SizeRelatedTreePruning cost = new SizeRelatedTreePruning(1);
    cost.calculateCost(t);
   
    Assert.assertEquals(17, t.getWeight(10, t.getNeighborIx(10, 5)),0.01);
    Assert.assertEquals(3, t.getWeight(6, t.getNeighborIx(6, 7)),0.01);
  }
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    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    final RNASpecificTree t = new RNASpecificTree("T");
    t.buildFromViennaFormat(
        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA"
            .toCharArray(),
        "((..((........))(((.....)))....(.......)))...."
            .toCharArray());
    final RNASpecificTree s = new RNASpecificTree("S");
    s.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    Random rand = new Random(123l);
    final RNASpecificTree sR = new RNASpecificTree("S-Random");
//    sR.buildFromViennaFormat(
//        "GGGAGUAUGUACCGAUAGGGUGAUUCCGGGCCCUUCGACNGGCUCCAUC"
//            .toCharArray(),
//        "(((((............((......))(((.))).(.....)))))).."
//            .toCharArray());
    sR.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    sR.shuffle(rand);
    sR.toFASTAFile("sR.fasta");
    sR.toDotFile("sR.dot", false);
    s.toDotFile("s.dot", false);
    t.toDotFile("t.dot", false);
    prune2.calculateCost(t);
    prune2.calculateCost(s);
    prune2.calculateCost(sR);
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    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    RNASpecificTree t = new RNASpecificTree();
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    t.buildFromViennaFormat(
        "NNNUAUAGUUUGAGUUCGAUUGCGCUUCGUAUGUUGCGUCUACGUAAAAACGCUCAGUUUAAAUUAUAACUGCAAAAAAUAAUAACAAUUCUUACGCUUUAGCUGCCUAAUAAGCGCUUAACGUAGAUCCUCCCAGGAUCGUCCAUGUUCUGGAUCUGGGUCCUAAAUUUAGUGGACUUACGCUCAAAGCUUCCACCUGGAGUUGCGAGAAGAGACUAAUCAGGUUAGUCAUUGCUGGGUGCCCUGUCAUACGGCGUUUGCAAUGAUGAAAUUUAAAUAGUAUGAAUAUGAGCGUAGAUAUCCGAGGGGCAAUAUGCUUAGACGCNNN"
            .toCharArray(),
        "...((((.......((((((..(((((........((((..........))))...........................................(.((((.(((.......))).)))).)..(((((..(((((((.......)))))))....)))))....................(((..((((.........))))..)))..................(((((...(((.((((.........))))).))..)))))......................))))).....)).))))......))))............"
            .toCharArray());

    prune.calculateCost(t);
    smooth.calculateCost(t);

    RNASpecificTree s = new RNASpecificTree();
    // s.buildFromViennaFormat("GGACCGAUGGUAGUGUCUUCGGAUGCGAGAGUAGGUC".toCharArray(),
    // ".((((((((((((((((....))))))))))))))))".toCharArray());
    // s.buildFromViennaFormat("GAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAUCCCCUC".toCharArray(),
    // "(((((((......)))))))(((((((......)))))))(((((((......)))))))(((((((.....)))))))".toCharArray());
    // s.buildFromViennaFormat("CCGGgGGAUCACCACGGCGGgGGAUCACCACGG".toCharArray(),
    // "((((.((....))))))(((.((....))))).".toCharArray());
    s.buildFromViennaFormat(
        "GGCGACACGGAUUCCAGUGCAUAUCUUAGUGAUACUCCAGUUAACUCCAUACUUUCCCUGCAAUACGCUAUUCGCCUCAGAUGUAUUUGGGUGGUUGCUCCACUAAAGCCCAGGAAUAUCCAGCCAGUUACAUUUGAGGCCAUUUGGGCUUAAGCGUAUUCCAUGGAAAGUUUUCUCCCCACAUUUCGGAAAUUAAAUUCCGAGCCAGCAAGAAAAUCUUCUCUGUUACAAUUUGACAUGGCUAAAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGGCGUAAUCUCAUACAAUGAUUACCCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAAAGUGUCUGACAUAAUCAAACAUUUGCACAUUCUUUGACCAAGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUGCAGACCAUAUGUUCCAGUUUCGGAGAUUUUUUGCUGCCAAACGGAAUACUUAUAAAAACCCACAUUCUAUUUACAUCACUAAGAAGAGCAUUGCAAUCUGUUUAGCC"
            .toCharArray(),
        "((((..(((((((.((((((...((((((((((.................(((((((.((.((((((((....((((((((((((.((((...((((.(((...........))).)).))..)))).))))))))))))............)))))))).)).)))))))........................(((((((...((((((((((.((((.((((..((((((((.((((((((.(((.((.....((((((.....((((((((.(((((((.(((((...........))))))))..))))..))))))))...........))))))..........)).))).)).)))))).))))(.(((((.(((.........((((((((((((.......))))).))..)))))...............)))))))))..))))..))))....)))))))))))))).....)))))))..........................))))))))))...)))))).)))))))..))))"
            .toCharArray());
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    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    final RNASpecificTree t = new RNASpecificTree("T");
    t.buildFromViennaFormat(
        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA".toCharArray(),
        "((..((........))(((.....)))....(.......)))....".toCharArray());
    final RNASpecificTree s = new RNASpecificTree("S");
    s.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    Random rand = new Random(123l);
    final RNASpecificTree sR = new RNASpecificTree("S-Random");
    sR.buildFromViennaFormat(
        "GAUAGAUGGUCUGGGUGUCGCCAGAUCGGGGUNCAAUUCCCCGUCGCCA"
            .toCharArray(),
        "((..(......)(((.....)))...(((((.......)))))))...."
            .toCharArray());
    sR.shuffle(rand);
    prune.calculateCost(t);
    prune.calculateCost(s);
    prune.calculateCost(sR);

    smooth.calculateCost(t);
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    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    final RNASpecificTree t = new RNASpecificTree("T");
    t.buildFromViennaFormat(
        "GGGGGGGGuuuAAAAAAAAAAcccUUUUUUUUUUuuuGGGGGGcccUUUUUUuuuCCCCCCCC"
            .toCharArray(),
        "((((((((...((((((((((...))))))))))...((((((...))))))...))))))))"
            .toCharArray());
    final RNASpecificTree s = new RNASpecificTree("S");
    s.buildFromViennaFormat(
        "UUUUUUUUUUuuuGGGGGGcccUUUUUUuuuCCCCCCCCcccGGGGGGGGuuuAAAAAAAAAA"
            .toCharArray(),
        "((((((((((...((((((...))))))...((((((((...))))))))...))))))))))"
            .toCharArray());
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    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    final RNASpecificTree t = new RNASpecificTree("T");
    /*t.buildFromViennaFormat(
        "UUUAGCAGUUGGGAGCGCCUGAAGGGAGGUCCUNCGAUCGAAACCA".toCharArray(),
        "((..((........))(((.....)))....(.......)))....".toCharArray());
        */
   
    t.buildFromViennaFormat(
        "GCCUGAAGGGACGCCUGAAGGGA".toCharArray(),
        "(((.....))).(((.....)))".toCharArray());
   
    prune.calculateCost(t);
    smooth.calculateCost(t);
   
    try {
      t.toDotFile("/home/milon/tmp/1.dot", true);
    } catch (IOException e) {
      // TODO Auto-generated catch block
      e.printStackTrace();
    }
 
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    RnaSpecificCostFunction cost = new RnaSpecificCostFunction(
        new ScoringMatrix("matrix" + File.separator
            + "bp-RIBOSUM85-60.matrix",
            RNABasePairAlphabet.getInstance()), aligner);

    RNASpecificTree t = new RNASpecificTree();
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    // t.buildFromViennaFormat("GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC".toCharArray(),
    // "((((((((.((((((..))))))...))))))))".toCharArray());
    t.buildFromViennaFormat(
        "NNNUAUAGUUUGAGUUCGAUUGCGCUUCGUAUGUUGCGUCUACGUAAAAACGCUCAGUUUAAAUUAUAACUGCAAAAAAUAAUAACAAUUCUUACGCUUUAGCUGCCUAAUAAGCGCUUAACGUAGAUCCUCCCAGGAUCGUCCAUGUUCUGGAUCUGGGUCCUAAAUUUAGUGGACUUACGCUCAAAGCUUCCACCUGGAGUUGCGAGAAGAGACUAAUCAGGUUAGUCAUUGCUGGGUGCCCUGUCAUACGGCGUUUGCAAUGAUGAAAUUUAAAUAGUAUGAAUAUGAGCGUAGAUAUCCGAGGGGCAAUAUGCUUAGACGCNNN"
            .toCharArray(),
        "...((((.......((((((..(((((........((((..........))))...........................................(.((((.(((.......))).)))).)..(((((..(((((((.......)))))))....)))))....................(((..((((.........))))..)))..................(((((...(((.((((.........))))).))..)))))......................))))).....)).))))......))))............"
            .toCharArray());

    prune.calculateCost(t);
    smooth.calculateCost(t);

    RNASpecificTree s = new RNASpecificTree();
    // s.buildFromViennaFormat("GGACCGAUGGUAGUGUCUUCGGAUGCGAGAGUAGGUC".toCharArray(),
    // ".((((((((((((((((....))))))))))))))))".toCharArray());
    // s.buildFromViennaFormat("GAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAUCCCCUC".toCharArray(),
    // "(((((((......)))))))(((((((......)))))))(((((((......)))))))(((((((.....)))))))".toCharArray());
    // s.buildFromViennaFormat("CCGGgGGAUCACCACGGCGGgGGAUCACCACGG".toCharArray(),
    // "((((.((....))))))(((.((....))))).".toCharArray());
    s.buildFromViennaFormat(
        "GGCGACACGGAUUCCAGUGCAUAUCUUAGUGAUACUCCAGUUAACUCCAUACUUUCCCUGCAAUACGCUAUUCGCCUCAGAUGUAUUUGGGUGGUUGCUCCACUAAAGCCCAGGAAUAUCCAGCCAGUUACAUUUGAGGCCAUUUGGGCUUAAGCGUAUUCCAUGGAAAGUUUUCUCCCCACAUUUCGGAAAUUAAAUUCCGAGCCAGCAAGAAAAUCUUCUCUGUUACAAUUUGACAUGGCUAAAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGGCGUAAUCUCAUACAAUGAUUACCCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAAAGUGUCUGACAUAAUCAAACAUUUGCACAUUCUUUGACCAAGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUGCAGACCAUAUGUUCCAGUUUCGGAGAUUUUUUGCUGCCAAACGGAAUACUUAUAAAAACCCACAUUCUAUUUACAUCACUAAGAAGAGCAUUGCAAUCUGUUUAGCC"
            .toCharArray(),
        "((((..(((((((.((((((...((((((((((.................(((((((.((.((((((((....((((((((((((.((((...((((.(((...........))).)).))..)))).))))))))))))............)))))))).)).)))))))........................(((((((...((((((((((.((((.((((..((((((((.((((((((.(((.((.....((((((.....((((((((.(((((((.(((((...........))))))))..))))..))))))))...........))))))..........)).))).)).)))))).))))(.(((((.(((.........((((((((((((.......))))).))..)))))...............)))))))))..))))..))))....)))))))))))))).....)))))))..........................))))))))))...)))))).)))))))..))))"
            .toCharArray());
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    int[][] correct = new int[][] { { 1 }, { 0, 2, 3, 17 }, { 1 },
        { 1, 4 }, { 3, 5 }, { 4, 6, 10, 11, 16 }, { 5, 7 }, { 6, 8 },
        { 7, 9 }, { 8 }, { 5 }, { 5, 12 }, { 11, 13 }, { 12, 14 },
        { 13, 15 }, { 14 }, { 5 }, { 1 } };

    RNASpecificTree tree = new RNASpecificTree();
    tree.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
        "...((((...))...(((...)))..))....".toCharArray());

    int[][] ans = tree.getEdges();
    Assert.assertEquals("The structure is not the same as expected", true,
        MatrixUtils.equals(ans, correct));
  }
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  }

  @Test
  public void testGroups() {

    RNASpecificTree tree = new RNASpecificTree();
    tree.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAA".toCharArray(),
        "...((((...))...(((...)))..))....".toCharArray());
    tree.groupByStructure();
    try {
      tree.toDotFile("/home/milon/tmp/1.dot", true);
    } catch (IOException e) {
      e.printStackTrace();
    }

    for (int t = 0; t < tree.getNodeNum(); t++) {
      int deg = tree.outDeg(t);
      RNANodeLabel tLabel = (RNANodeLabel) tree.getLabel(t);
      for (int d = 0; d < deg; d++) {
        int v = tree.getNeighbor(t, d);
        RNANodeLabel vLabel = (RNANodeLabel) tree.getLabel(v);
        if ((tLabel.getType() == RNANodeLabel.BASE_PAIR && vLabel
            .getType() == RNANodeLabel.BASE_PAIR)) {
          Assert.assertEquals("Should have the same group", true,
              tLabel.getGroup() == vLabel.getGroup());
        }
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    }
  }

  @Test
  public void testEquals() {
    RNASpecificTree tree1 = new RNASpecificTree();
    tree1.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree2 = new RNASpecificTree();
    tree2.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUUUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree3 = new RNASpecificTree();
    tree3.buildFromViennaFormat(
        "CGACAGGAAACUGACAAACCCUAUCAUCUUAAAUAUAUGGGCGAUAUAU"
            .toCharArray(),
        "...((((...))...(((...)))..))....((((((.....))))))"
            .toCharArray());
    RNASpecificTree tree4 = new RNASpecificTree();
    tree4.buildFromViennaFormat("CGACAGGAAACUGACAA".toCharArray(),
        "...((((...))))...".toCharArray());

    Assert.assertEquals("Trees should be the same", true,
        tree1.equals(tree2));
    Assert.assertEquals("Trees should not be the same", false,
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Related Classes of bgu.bio.adt.rna.RNASpecificTree

  • bgu.bio.adt.rna.TestRNASpecificTree
  • bgu.bio.algorithms.graphs.costs.TestSizeRelatedCostCalculator
  • bgu.bio.algorithms.graphs.Test
  • bgu.bio.algorithms.graphs.TestHSA
  • bgu.bio.ds.rna.RNA
  • gnu.trove.list.array.TCharArrayList
  • gnu.trove.list.array.TIntArrayList
  • java.io.Writer
  • java.io.FileWriter
  • java.util.Random
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