tests for writing out sequences based on VCF data

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15732 ee4ac58c-ac51-4696-9907-e4b3aa274f04

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

+
+package uk.ac.sanger.artemis.components.variant;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.net.URL;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+
+import junit.framework.Assert;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.Selection;
+import uk.ac.sanger.artemis.SimpleEntryGroup;
+import uk.ac.sanger.artemis.components.EntryFileDialog;
+import uk.ac.sanger.artemis.components.variant.VCFview;
+import uk.ac.sanger.artemis.io.EntryInformation;
+import uk.ac.sanger.artemis.sequence.MarkerRange;
+import uk.ac.sanger.artemis.sequence.Strand;
+import uk.ac.sanger.artemis.util.Document;
+import uk.ac.sanger.artemis.util.DocumentFactory;
+
+/**
+ * Tests for writing out sequences based on VCF data.
+ */
+public class WriteVCFTest
+{
+  private VCFview vcfView;
+  
+  /**
+   * Write FASTA, from a range selection on the forward strand.
+   * Variation is a SNP.
+   * VCF line : test    120768  .       C       T
+   */
+  @Test
+  public void testWriteFwdFastaSNP()
+  {
+    StringWriter writer = getWriter(true, 120768, 120777);
+    
+    StringBuffer buff = new StringBuffer("> test.embl.gz 120768:120777\n");
+    buff.append("cttgtcaagg\n");
+    buff.append(">test.vcf.gz test.embl.gz 120768:120777\n");
+    buff.append("tttgtcaagg\n");
+    assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+  }
+  
+  /**
+   * Write FASTA, from a range selection on the reverse strand.
+   * Variation is a SNP.
+   * VCF line : test    120768  .       C       T
+   */
+  @Test
+  public void testWriteRevFastaSNP()
+  {
+    StringWriter writer = getWriter(false, 120768, 120777);
+
+    StringBuffer buff = new StringBuffer("> test.embl.gz 120768:120777 reverse\n");
+    buff.append("ccttgacaag\n");
+    buff.append(">test.vcf.gz test.embl.gz 120768:120777 reverse\n");
+    buff.append("ccttgacaaa\n");
+    assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+  }
+  
+  /**
+   * Write FASTA, from a range selection on the forward strand.
+   * Variation is a deletion.
+   * test    396838  .       tt      t
+   */
+  @Test
+  public void testWriteFwdFastaDeletion()
+  {
+    StringWriter writer = getWriter(true, 396835, 396845);
+
+    StringBuffer buff = new StringBuffer("> test.embl.gz 396835:396845\n");
+    buff.append("tttttaggtat\n");
+    buff.append(">test.vcf.gz test.embl.gz 396835:396845\n");
+    buff.append("tttt-aggtat\n");
+    assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+  }
+  
+  /**
+   * Write FASTA, from a range selection on the reverse strand.
+   * Variation is a deletion.
+   * test    396838  .       tt      t
+   */
+  @Test
+  public void testWriteRevFastaDeletion()
+  {
+    StringWriter writer = getWriter(false, 396835, 396845);
+
+    StringBuffer buff = new StringBuffer("> test.embl.gz 396835:396845 reverse\n");
+    buff.append("atacctaaaaa\n");
+    buff.append(">test.vcf.gz test.embl.gz 396835:396845 reverse\n");
+    buff.append("ataccta-aaa\n");
+    assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+  }
+  
+  /**
+   * Write FASTA, from a range selection on the forward strand.
+   * Variation is a insertion.
+   * test    366787  .       t       tT
+   */
+  @Test
+  public void testWriteFwdFastaInsertion()
+  {
+    StringWriter writer = getWriter(true, 366785, 366795);
+
+    StringBuffer buff = new StringBuffer("> test.embl.gz 366785:366795\n");
+    buff.append("tttcgcttttt\n");
+    buff.append(">test.vcf.gz test.embl.gz 366785:366795\n");
+    buff.append("tttTcgcttttt\n");
+    assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+  }
+  
+  /**
+   * Write FASTA, from a range selection on the reverse strand.
+   * Variation is a insertion.
+   * test    366787  .       t       tT
+   */
+  @Test
+  public void testWriteRevFastaInsertion()
+  {
+    StringWriter writer = getWriter(false, 366785, 366795);
+
+    StringBuffer buff = new StringBuffer("> test.embl.gz 366785:366795 reverse\n");
+    buff.append("aaaaagcgaaa\n");
+    buff.append(">test.vcf.gz test.embl.gz 366785:366795 reverse\n");
+    buff.append("aaaaagcgaaaa\n");
+    assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+  }
+  
+  
+  /**
+   * Write FASTA, from a range selection on the forward strand.
+   * Variation is a multiple allele, (PL number indicates either G or T):
+   * test    361978  .       G       T       77.76842        .       DP=11;AF1=0.95;CI95=0.5,1;DP4=1,0,10,0;MQ=58;PV4=1,9.6e-06,0.37,1       PL:DP:SP:GT:GQ  106,0,0:11:0:1/1:10
+   */
+  @Test
+  public void testWriteFwdFastaMultipleAllele()
+  {
+    StringWriter writer = getWriter(true, 361975, 361985);
+
+    StringBuffer buff = new StringBuffer("> test.embl.gz 361975:361985\n");
+    buff.append("actgaaaaatt\n");
+    buff.append(">test.vcf.gz test.embl.gz 361975:361985\n");
+    buff.append("actkaaaaatt\n");
+    assertEquals("Export FASTA range ", writer.toString(), buff.toString());
+  }
+  
+  
+  /**
+   * G
+   * @param isFwd
+   * @param start
+   * @param end
+   * @return
+   */
+  private StringWriter getWriter(boolean isFwd, int start, int end)
+  {
+    StringWriter writer = new StringWriter();
+    Selection selection = new Selection(null);
+    
+    FeatureVector features = vcfView.getEntryGroup().getAllFeatures();
+    Feature feature = null;
+    for(int i=0; i<features.size(); i++)
+    {
+      if(features.elementAt(i).isForwardFeature() && isFwd)
+      {
+        feature = features.elementAt(i);
+        break;
+      }
+      else if(!features.elementAt(i).isForwardFeature() && !isFwd)
+      {
+        feature = features.elementAt(i);
+        
+        int length = vcfView.getEntryGroup().getSequenceEntry().getBases().getLength();
+        int tmp = start;
+        start = length - end + 1;
+        end   = length - tmp + 1;
+
+        break;
+      }
+    }
+
+    try
+    {
+      selection.setMarkerRange(new MarkerRange(feature.getStrand(), start, end));
+    }
+    catch(uk.ac.sanger.artemis.util.OutOfRangeException e)
+    {
+      e.printStackTrace();
+    }
+    IOUtils.exportFastaByRange(vcfView, selection, false, writer);
+    return writer;
+  }
+  
+  
+  /**
+   * Open a flat file and create the components in the TransferAnnotaionTool
+   * used to control the transfer of annotation.
+   */
+  @Before
+  public void setup()
+  {
+    final URL ref = WriteVCFTest.class.getResource("/data/test.embl.gz");
+    final URL vcf = WriteVCFTest.class.getResource("/data/test.vcf.gz");
+  
+    List<String> vcfFileList = new Vector<String>();
+    vcfFileList.add(vcf.getFile());
+    JFrame f = new JFrame();
+    vcfView = new VCFview(f, (JPanel) f.getContentPane(), 
+        vcfFileList, 
+        5000, 100000000, null, 
+        ref.getFile(), null);
+    f.setVisible(false);
+  }
+
+}
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