tests for writing variant sites

test/uk/ac/sanger/artemis/components/variant/WriteVariantSitesTest.java

+package uk.ac.sanger.artemis.components.variant;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.FileOutputStream;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.net.URL;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.components.variant.VCFview;
+import uk.ac.sanger.artemis.sequence.Bases;
+
+
+public class WriteVariantSitesTest
+{ 
+  /**
+   * Test SNP's
+   */
+  @Test
+  public void testSNPSites()
+  {
+    // load VCF
+    final URL ref = WriteVCFTest.class.getResource("/data/test.embl.gz");
+    final URL vcf = WriteVCFTest.class.getResource("/data/test1.vcf.gz");
+    VCFview vcfView = getVcfView(ref, vcf);
+    
+    StringWriter sw = new StringWriter();
+    PrintWriter pw  = new PrintWriter(sw);
+
+    EntryGroup entryGroup = vcfView.getEntryGroup();
+    
+    IOUtils.exportVariantFasta(vcfView, pw, 
+        entryGroup.getSequenceEntry().getBases().getLength(), 
+        entryGroup.getAllFeatures(), 
+        entryGroup.getSequenceEntry().getBases());
+
+    StringBuilder fastaBuff = new StringBuilder(">1_sample\n");
+    fastaBuff.append("TTTTGAACTTATACA\n");
+    fastaBuff.append(">test.embl.gz\n");
+    fastaBuff.append("CCCCATGTGGGCGTG\n");
+    
+    assertEquals("Export variants as FASTA ", sw.toString(), fastaBuff.toString());
+  }
+  
+  /**
+   * Test insertions
+   */
+  @Test
+  public void testInsertionSites()
+  {
+    // load VCF
+    final URL ref = WriteVCFTest.class.getResource("/data/test.embl.gz");
+    final URL vcf = WriteVCFTest.class.getResource("/data/test2.vcf.gz");
+    VCFview vcfView = getVcfView(ref, vcf);
+    
+    StringWriter sw = new StringWriter();
+    PrintWriter pw  = new PrintWriter(sw);
+
+    EntryGroup entryGroup = vcfView.getEntryGroup();
+    
+    IOUtils.exportVariantFasta(vcfView, pw, 
+        entryGroup.getSequenceEntry().getBases().getLength(), 
+        entryGroup.getAllFeatures(), 
+        entryGroup.getSequenceEntry().getBases());
+
+    StringBuilder fastaBuff = new StringBuilder(">1_sample\n");
+    fastaBuff.append("tGgTttttttAaaTttaAGAaAGTAGa\n");
+    fastaBuff.append(">test.embl.gz\n");
+    fastaBuff.append("t-gttttt-ta-att-a---aa-----\n");
+    
+    assertEquals("Export variants as FASTA ", sw.toString(), fastaBuff.toString());
+  }
+  
+  /**
+   * Test Multi-allele
+   */
+  @Test
+  public void testMultiAlleleSites()
+  {
+    // load VCF
+    final URL ref = WriteVCFTest.class.getResource("/data/test.embl.gz");
+    final URL vcf = WriteVCFTest.class.getResource("/data/test3.vcf.gz");
+    VCFview vcfView = getVcfView(ref, vcf);
+    
+    StringWriter sw = new StringWriter();
+    PrintWriter pw  = new PrintWriter(sw);
+
+    EntryGroup entryGroup = vcfView.getEntryGroup();
+    
+    IOUtils.exportVariantFasta(vcfView, pw, 
+        entryGroup.getSequenceEntry().getBases().getLength(), 
+        entryGroup.getAllFeatures(), 
+        entryGroup.getSequenceEntry().getBases());
+
+    StringBuilder fastaBuff = new StringBuilder(">1_sample\n");
+    fastaBuff.append("wwmrwr\n");
+    fastaBuff.append(">test.embl.gz\n");
+    fastaBuff.append("ggtgcc\n");
+    
+    assertEquals("Export variants as FASTA ", sw.toString(), fastaBuff.toString());
+  }
+  
+  
+  /**
+   * Test deletion. Note: do not write out if just deletion.
+   */
+  @Test
+  public void testDeletionSites()
+  {
+    // load VCF
+    final URL ref = WriteVCFTest.class.getResource("/data/test.embl.gz");
+    final URL vcf = WriteVCFTest.class.getResource("/data/test4.vcf.gz");
+    VCFview vcfView = getVcfView(ref, vcf);
+    
+    StringWriter sw = new StringWriter();
+    PrintWriter pw  = new PrintWriter(sw);
+
+    EntryGroup entryGroup = vcfView.getEntryGroup();
+    
+    IOUtils.exportVariantFasta(vcfView, pw, 
+        entryGroup.getSequenceEntry().getBases().getLength(), 
+        entryGroup.getAllFeatures(), 
+        entryGroup.getSequenceEntry().getBases());
+
+    StringBuilder fastaBuff = new StringBuilder(">1_sample\n");
+    fastaBuff.append(">test.embl.gz\n");
+    
+    assertEquals("Export variants as FASTA ", sw.toString(), fastaBuff.toString());
+  }
+  
+  /**
+   * Load in a VCF and BCF into separate VCFviews to be used 
+   * separately in testing.
+   */
+  private VCFview getVcfView(final URL ref, final URL vcf)
+  {
+    List<String> vcfFileList = new Vector<String>();
+    vcfFileList.add(vcf.getFile());
+
+    return new VCFview(null, new JPanel(), 
+        vcfFileList, 
+        5000, 100000000, null, 
+        ref.getFile(), null, null);
+    
+    // load BCF
+/*    ref = WriteVCFTest.class.getResource("/data/MAL1.embl.gz");
+    vcf = WriteVCFTest.class.getResource("/data/MAL1_8_16_24h.raw.bcf");
+    
+    List<String> bcfFileList = new Vector<String>();
+    bcfFileList.add(vcf.getFile());
+    bcfView = new VCFview(null, new JPanel(), 
+        bcfFileList, 
+        5000, 100000000, null, 
+        ref.getFile(), null, null);*/
+  }
+}
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