test/jalview/analysis/DnaTest.java

   1 package jalview.analysis;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import static org.junit.Assert.assertNotNull;
   5 import static org.junit.Assert.assertTrue;
   6 import jalview.api.AlignViewportI;
   7 import jalview.datamodel.AlignedCodon;
   8 import jalview.datamodel.AlignmentI;
   9 import jalview.datamodel.ColumnSelection;
  10 import jalview.gui.AlignViewport;
  11 import jalview.io.FormatAdapter;
  12
  13 import java.io.IOException;
  14
  15 import org.junit.Test;
  16
  17 public class DnaTest
  18 {
  19   // @formatter:off
  20   // AA encoding codons as ordered on the Jalview help page Amino Acid Table
  21   private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
  22           + "TGT" + "TGC" + "GAT" + "GAC" + "GAA" + "GAG" + "TTT" + "TTC"
  23           + "GGT" + "GGC" + "GGA" + "GGG" + "CAT" + "CAC" + "ATT" + "ATC"
  24           + "ATA" + "AAA" + "AAG" + "TTG" + "TTA" + "CTT" + "CTC" + "CTA"
  25           + "CTG" + "ATG" + "AAT" + "AAC" + "CCT" + "CCC" + "CCA" + "CCG"
  26           + "CAA" + "CAG" + "CGT" + "CGC" + "CGA" + "CGG" + "AGA" + "AGG"
  27           + "TCT" + "TCC" + "TCA" + "TCG" + "AGT" + "AGC" + "ACT" + "ACC"
  28           + "ACA" + "ACG" + "GTT" + "GTC" + "GTA" + "GTG" + "TGG" + "TAT"
  29           + "TAC" + "TAA" + "TAG" + "TGA";
  30
  31   private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
  32           + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  33           + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
  34           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  35           + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
  36           + ">gi|27804621|gb|AY178912.1|/1-259\n"
  37           + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  38           + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
  39           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  40           + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
  41           + ">gi|27804623|gb|AY178913.1|/1-259\n"
  42           + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  43           + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
  44           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  45           + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  46           + ">gi|27804627|gb|AY178915.1|/1-260\n"
  47           + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  48           + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
  49           + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
  50           + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
  51           + ">gi|27804631|gb|AY178917.1|/1-261\n"
  52           + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  53           + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
  54           + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  55           + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
  56           + ">gi|27804635|gb|AY178919.1|/1-261\n"
  57           + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
  58           + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
  59           + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  60           + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  61           + ">gi|27804641|gb|AY178922.1|/1-261\n"
  62           + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  63           + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
  64           + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  65           + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
  66           + ">gi|27804647|gb|AY178925.1|/1-261\n"
  67           + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
  68           + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
  69           + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
  70           + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
  71           + ">gi|27804649|gb|AY178926.1|/1-261\n"
  72           + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  73           + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
  74           + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
  75           + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
  76           + ">gi|27804653|gb|AY178928.1|/1-261\n"
  77           + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  78           + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
  79           + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
  80           + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
  81           + ">gi|27804659|gb|AY178931.1|/1-261\n"
  82           + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  83           + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
  84           + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  85           + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
  86   // @formatter:on
  87
  88   /**
  89    * Corner case for this test is the presence of codons after codons that were
  90    * not translated.
  91    *
  92    * @throws IOException
  93    */
  94   @Test
  95   public void testTranslateCdna_withUntranslatableCodons()
  96           throws IOException
  97   {
  98     AlignmentI alf = new FormatAdapter().readFile(
  99             JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
 100             "FASTA");
 101     ColumnSelection cs = new ColumnSelection();
 102     AlignViewportI av = new AlignViewport(alf, cs);
 103     Dna dna = new Dna(av, new int[]
 104     { 0, alf.getWidth() - 1 });
 105     AlignmentI translated = dna.translateCdna();
 106     assertNotNull("Couldn't do a full width translation of test data.",
 107             translated);
 108   }
 109
 110   /**
 111    * Test variant in which 15 column blocks at a time are translated (the rest
 112    * hidden).
 113    *
 114    * @throws IOException
 115    */
 116   @Test
 117   public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns()
 118           throws IOException
 119   {
 120     AlignmentI alf = new FormatAdapter().readFile(
 121             JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE,
 122             "FASTA");
 123     int vwidth = 15;
 124     for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth)
 125     {
 126       ColumnSelection cs = new ColumnSelection();
 127       if (ipos > 0)
 128       {
 129         cs.hideColumns(0, ipos - 1);
 130       }
 131       cs.hideColumns(ipos + vwidth, alf.getWidth());
 132       int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
 133       AlignViewportI av = new AlignViewport(alf, cs);
 134       Dna dna = new Dna(av, vcontigs);
 135       AlignmentI transAlf = dna.translateCdna();
 136
 137       assertTrue("Translation failed (ipos=" + ipos
 138               + ") No alignment data.", transAlf != null);
 139       assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
 140               transAlf.getHeight() > 0);
 141       assertTrue("Translation failed (ipos=" + ipos + ") Translated "
 142               + transAlf.getHeight() + " sequences from " + alf.getHeight()
 143               + " sequences", alf.getHeight() == transAlf.getHeight());
 144     }
 145   }
 146
 147   /**
 148    * Test simple translation to Amino Acids (with STOP codons translated to X).
 149    *
 150    * @throws IOException
 151    */
 152   @Test
 153   public void testTranslateCdna_simple() throws IOException
 154   {
 155     AlignmentI alf = new FormatAdapter().readFile(fasta,
 156             FormatAdapter.PASTE, "FASTA");
 157     ColumnSelection cs = new ColumnSelection();
 158     AlignViewportI av = new AlignViewport(alf, cs);
 159     Dna dna = new Dna(av, new int[]
 160     { 0, alf.getWidth() - 1 });
 161     AlignmentI translated = dna.translateCdna();
 162     String aa = translated.getSequenceAt(0).getSequenceAsString();
 163     assertEquals(
 164             "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYYXXX",
 165             aa);
 166   }
 167
 168   /**
 169    * Test translation excluding hidden columns.
 170    *
 171    * @throws IOException
 172    */
 173   @Test
 174   public void testTranslateCdna_hiddenColumns() throws IOException
 175   {
 176     AlignmentI alf = new FormatAdapter().readFile(fasta,
 177             FormatAdapter.PASTE, "FASTA");
 178     ColumnSelection cs = new jalview.datamodel.ColumnSelection();
 179     cs.hideColumns(6, 14); // hide codons 3/4/5
 180     cs.hideColumns(24, 35); // hide codons 9-12
 181     cs.hideColumns(177, 191); // hide codons 60-64
 182     AlignViewportI av = new AlignViewport(alf, cs);
 183     Dna dna = new Dna(av, new int[]
 184     { 0, alf.getWidth() - 1 });
 185     AlignmentI translated = dna.translateCdna();
 186     String aa = translated.getSequenceAt(0).getSequenceAsString();
 187     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
 188   }
 189
 190   /**
 191    * Use this test to help debug into any cases of interest.
 192    */
 193   @Test
 194   public void testCompareCodonPos_oneOnly()
 195   {
 196     assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
 197   }
 198
 199   /**
 200    * Tests for method that compares 'alignment' of two codon position triplets.
 201    */
 202   @Test
 203   public void testCompareCodonPos()
 204   {
 205     /*
 206      * Returns 0 for any null argument
 207      */
 208     assertEquals(0, Dna.compareCodonPos(new AlignedCodon(1, 2, 3), null));
 209     assertEquals(0, Dna.compareCodonPos(null, new AlignedCodon(1, 2, 3)));
 210
 211     /*
 212      * Work through 27 combinations. First 9 cases where first position matches.
 213      */
 214     assertMatches("AAA", "GGG"); // 2 and 3 match
 215     assertFollows("AA-A", "GGG"); // 2 matches, 3 shifted seq1
 216     assertPrecedes("AAA", "GG-G"); // 2 matches, 3 shifted seq2
 217     assertFollows("A-AA", "GG-G"); // 2 shifted seq1, 3 matches
 218     assertFollows("A-A-A", "GG-G"); // 2 shifted seq1, 3 shifted seq1
 219     assertPrecedes("A-AA", "GG--G"); // 2 shifted seq1, 3 shifted seq2
 220     assertPrecedes("AA-A", "G-GG"); // 2 shifted seq2, 3 matches
 221     assertFollows("AA--A", "G-GG"); // 2 shifted seq2, 3 shifted seq1
 222     assertPrecedes("AAA", "G-GG"); // 2 shifted seq2, 3 shifted seq2
 223
 224     /*
 225      * 9 cases where first position is shifted in first sequence.
 226      */
 227     assertFollows("-AAA", "G-GG"); // 2 and 3 match
 228     assertFollows("-AA-A", "G-GG"); // 2 matches, 3 shifted seq1
 229     // 'enclosing' case: pick first to start precedes
 230     assertFollows("-AAA", "G-G-G"); // 2 matches, 3 shifted seq2
 231     assertFollows("-A-AA", "G-G-G"); // 2 shifted seq1, 3 matches
 232     assertFollows("-A-A-A", "G-G-G"); // 2 shifted seq1, 3 shifted seq1
 233     // 'enclosing' case: pick first to start precedes
 234     assertFollows("-A-AA", "G-G--G"); // 2 shifted seq1, 3 shifted seq2
 235     assertFollows("-AA-A", "G--GG"); // 2 shifted seq2, 3 matches
 236     assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1
 237     assertPrecedes("-AAA", "G--GG"); // 2 shifted seq2, 3 shifted seq2
 238
 239     /*
 240      * 9 cases where first position is shifted in second sequence.
 241      */
 242     assertPrecedes("A-AA", "-GGG"); // 2 and 3 match
 243     assertPrecedes("A-A-A", "-GGG"); // 2 matches, 3 shifted seq1
 244     assertPrecedes("A-AA", "-GG-G"); // 2 matches, 3 shifted seq2
 245     assertPrecedes("A--AA", "-GG-G"); // 2 shifted seq1, 3 matches
 246     // 'enclosing' case with middle base deciding:
 247     assertFollows("A--AA", "-GGG"); // 2 shifted seq1, 3 shifted seq1
 248     assertPrecedes("A--AA", "-GG--G"); // 2 shifted seq1, 3 shifted seq2
 249     assertPrecedes("AA-A", "-GGG"); // 2 shifted seq2, 3 matches
 250     assertPrecedes("AA--A", "-GGG"); // 2 shifted seq2, 3 shifted seq1
 251     assertPrecedes("AAA", "-GGG"); // 2 shifted seq2, 3 shifted seq2
 252   }
 253
 254   /**
 255    * Test that all the cases in testCompareCodonPos have a 'symmetric'
 256    * comparison (without checking the actual comparison result).
 257    */
 258   @Test
 259   public void testCompareCodonPos_isSymmetric()
 260   {
 261     assertSymmetric("AAA", "GGG");
 262     assertSymmetric("AA-A", "GGG");
 263     assertSymmetric("AAA", "GG-G");
 264     assertSymmetric("A-AA", "GG-G");
 265     assertSymmetric("A-A-A", "GG-G");
 266     assertSymmetric("A-AA", "GG--G");
 267     assertSymmetric("AA-A", "G-GG");
 268     assertSymmetric("AA--A", "G-GG");
 269     assertSymmetric("AAA", "G-GG");
 270     assertSymmetric("-AAA", "G-GG");
 271     assertSymmetric("-AA-A", "G-GG");
 272     assertSymmetric("-AAA", "G-G-G");
 273     assertSymmetric("-A-AA", "G-G-G");
 274     assertSymmetric("-A-A-A", "G-G-G");
 275     assertSymmetric("-A-AA", "G-G--G");
 276     assertSymmetric("-AA-A", "G--GG");
 277     assertSymmetric("-AA--A", "G--GG");
 278     assertSymmetric("-AAA", "G--GG");
 279     assertSymmetric("A-AA", "-GGG");
 280     assertSymmetric("A-A-A", "-GGG");
 281     assertSymmetric("A-AA", "-GG-G");
 282     assertSymmetric("A--AA", "-GG-G");
 283     assertSymmetric("A--AA", "-GGG");
 284     assertSymmetric("A--AA", "-GG--G");
 285     assertSymmetric("AA-A", "-GGG");
 286     assertSymmetric("AA--A", "-GGG");
 287     assertSymmetric("AAA", "-GGG");
 288   }
 289
 290   private void assertSymmetric(String codon1, String codon2)
 291   {
 292     assertEquals("Comparison of '" + codon1 + "' and '" + codon2
 293             + " not symmetric", Integer.signum(compare(codon1, codon2)),
 294             -Integer.signum(compare(codon2, codon1)));
 295   }
 296
 297   /**
 298    * Assert that the first sequence should map to the same position as the
 299    * second in a translated alignment. Also checks that this is true if the
 300    * order of the codons is reversed.
 301    *
 302    * @param codon1
 303    * @param codon2
 304    */
 305   private void assertMatches(String codon1, String codon2)
 306   {
 307     assertEquals("Expected '" + codon1 + "' matches '" + codon2 + "'", 0,
 308             compare(codon1, codon2));
 309     assertEquals("Expected '" + codon2 + "' matches '" + codon1 + "'", 0,
 310             compare(codon2, codon1));
 311   }
 312
 313   /**
 314    * Assert that the first sequence should precede the second in a translated
 315    * alignment
 316    *
 317    * @param codon1
 318    * @param codon2
 319    */
 320   private void assertPrecedes(String codon1, String codon2)
 321   {
 322     assertEquals("Expected '" + codon1 + "'  precedes '" + codon2 + "'",
 323             -1, compare(codon1, codon2));
 324   }
 325
 326   /**
 327    * Assert that the first sequence should follow the second in a translated
 328    * alignment
 329    *
 330    * @param codon1
 331    * @param codon2
 332    */
 333   private void assertFollows(String codon1, String codon2)
 334   {
 335     assertEquals("Expected '" + codon1 + "'  follows '" + codon2 + "'", 1,
 336             compare(codon1, codon2));
 337   }
 338
 339   /**
 340    * Convert two nucleotide strings to base positions and pass to
 341    * Dna.compareCodonPos, return the result.
 342    *
 343    * @param s1
 344    * @param s2
 345    * @return
 346    */
 347   private int compare(String s1, String s2)
 348   {
 349     final AlignedCodon cd1 = convertCodon(s1);
 350     final AlignedCodon cd2 = convertCodon(s2);
 351     System.out.println("K: " + s1 + "  " + cd1.toString());
 352     System.out.println("G: " + s2 + "  " + cd2.toString());
 353     System.out.println();
 354     return Dna.compareCodonPos(cd1, cd2);
 355   }
 356
 357   /**
 358    * Convert a string e.g. "-GC-T" to base positions e.g. [1, 2, 4]. The string
 359    * should have exactly 3 non-gap characters, and use '-' for gaps.
 360    *
 361    * @param s
 362    * @return
 363    */
 364   private AlignedCodon convertCodon(String s)
 365   {
 366     int[] codon = new int[3];
 367     int i = 0;
 368     for (int j = 0; j < s.length(); j++)
 369     {
 370       if (s.charAt(j) != '-')
 371       {
 372         codon[i++] = j;
 373       }
 374     }
 375     return new AlignedCodon(codon[0], codon[1], codon[2]);
 376   }
 377
 378   /**
 379    * Weirdly, maybe worth a test to prove the helper method of this test class.
 380    */
 381   @Test
 382   public void testConvertCodon()
 383   {
 384     assertEquals("[0, 1, 2]", convertCodon("AAA").toString());
 385     assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
 386     assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
 387   }
 388 }