test/jalview/analysis/DnaTranslation.java

   1 package jalview.analysis;
   2
   3 import static org.junit.Assert.*;
   4 import jalview.datamodel.ColumnSelection;
   5
   6 import java.io.IOException;
   7
   8 import org.junit.AfterClass;
   9 import org.junit.BeforeClass;
  10 import org.junit.Test;
  11 import org.junit.runner.RunWith;
  12
  13 public class DnaTranslation
  14 {
  15
  16   private static String JAL_1312_example_align_fasta =
  17           ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n"
  18                   +"ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  19                   +"GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n"
  20                   +"GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  21                   +"TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n"
  22                   +">gi|27804621|gb|AY178912.1|/1-259\n"
  23                   +"-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  24                   +"AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n"
  25                   +"GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  26                   +"TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n"
  27                   +">gi|27804623|gb|AY178913.1|/1-259\n"
  28                   +"-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n"
  29                   +"AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n"
  30                   +"GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  31                   +"TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  32                   +">gi|27804627|gb|AY178915.1|/1-260\n"
  33                   +"-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  34                   +"GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n"
  35                   +"GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n"
  36                   +"TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n"
  37                   +">gi|27804631|gb|AY178917.1|/1-261\n"
  38                   +"-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  39                   +"GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n"
  40                   +"GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  41                   +"TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n"
  42                   +">gi|27804635|gb|AY178919.1|/1-261\n"
  43                   +"-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n"
  44                   +"AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n"
  45                   +"GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  46                   +"TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n"
  47                   +">gi|27804641|gb|AY178922.1|/1-261\n"
  48                   +"-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  49                   +"GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n"
  50                   +"GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  51                   +"TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n"
  52                   +">gi|27804647|gb|AY178925.1|/1-261\n"
  53                   +"-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n"
  54                   +"GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
  55                   +"GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n"
  56                   +"TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n"
  57                   +">gi|27804649|gb|AY178926.1|/1-261\n"
  58                   +"-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n"
  59                   +"GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n"
  60                   +"GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n"
  61                   +"TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n"
  62                   +">gi|27804653|gb|AY178928.1|/1-261\n"
  63                   +"-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  64                   +"GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n"
  65                   +"GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n"
  66                   +"TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n"
  67                   +">gi|27804659|gb|AY178931.1|/1-261\n"
  68                   +"-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n"
  69                   +"GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n"
  70                   +"GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n"
  71                   +"TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n";
  72   @Test
  73   public void translationWithUntranslatableCodonsTest() {
  74     // Corner case for this test is the presence of codons after codons that were not translated.
  75     try {
  76       jalview.datamodel.AlignmentI alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE, "FASTA");
  77       int vwidth=15; // translate in 15 base stretches
  78       for (int ipos=0;ipos+vwidth<alf.getWidth();ipos+=vwidth) {
  79         ColumnSelection cs = new jalview.datamodel.ColumnSelection();
  80         if (ipos>0) { cs.hideColumns(0,ipos-1); }
  81         cs.hideColumns(ipos+vwidth,alf.getWidth());
  82         int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
  83         String[] sel = cs.getVisibleSequenceStrings(0, alf.getWidth(), alf.getSequencesArray());
  84       jalview.datamodel.AlignmentI transAlf = jalview.analysis.Dna.CdnaTranslate(alf.getSequencesArray(), sel,
  85               vcontigs, alf.getGapCharacter(),null, alf.getWidth(), null);
  86
  87       assertTrue("Translation failed (ipos="+ipos+") No alignment data.",transAlf!=null);
  88       assertTrue("Translation failed (ipos="+ipos+") Empty algnment.",transAlf.getHeight()>0);
  89       assertTrue("Translation failed (ipos="+ipos+") Translated "+transAlf.getHeight()+" sequences from "+alf.getHeight()+" sequences",alf.getHeight()==transAlf.getHeight());
  90       }
  91     } catch (IOException x)
  92     {
  93       x.printStackTrace();
  94       fail("Unexpected IOException ("+x.getMessage()+") - check test environment");
  95     }
  96   }
  97
  98 }