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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());