diff --git a/uk/ac/sanger/artemis/components/variant/BCFReader.java b/uk/ac/sanger/artemis/components/variant/BCFReader.java
index 4e49e9314224c3108f5e1b5b5fe963c37d60406e..b746e9a5e789f75c9cea283f49d4592f6ef50900 100644
--- a/uk/ac/sanger/artemis/components/variant/BCFReader.java
+++ b/uk/ac/sanger/artemis/components/variant/BCFReader.java
@@ -194,10 +194,10 @@ class BCFReader extends AbstractVCFReader
if(formatPattern.matcher(bcfRecord.getFormat()).matches())
{
- int n_alleles = bcfRecord.getNumAlleles();
+ int n_alleles = bcfRecord.getAlt().getNumAlleles();
int nc = (int) (n_alleles * ((float)(((float)n_alleles+1.f)/2.f)));
- if(bcfRecord.getAlt().equals("."))
+ if(bcfRecord.getAlt().isNonVariant())
nc = 1;
String fmts[] = bcfRecord.getFormat().split(":");
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index c48a00a19e335d10a7de827582d82dbca9899add..f18f9b83f721f9eb3a71fea9ea507b51b575b458 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -29,8 +29,6 @@ import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
-import java.util.Enumeration;
-import java.util.Hashtable;
import java.util.List;
import javax.swing.JFileChooser;
@@ -46,7 +44,6 @@ import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.components.StickyFileChooser;
import uk.ac.sanger.artemis.components.variant.BCFReader.BCFReaderIterator;
-import uk.ac.sanger.artemis.io.FastaStreamSequence;
import uk.ac.sanger.artemis.io.Key;
import net.sf.samtools.util.BlockCompressedInputStream;
@@ -67,7 +64,7 @@ class IOUtils
{
try
{
- File filterFile = getFile(vcfFileName, nfiles);
+ File filterFile = getFile(vcfFileName, nfiles, "filter");
FileWriter writer = new FileWriter(filterFile);
if(IOUtils.isBCF(vcfFileName))
{
@@ -101,13 +98,13 @@ class IOUtils
}
}
- private static File getFile(final String vcfFileName, final int nfiles) throws IOException
+ private static File getFile(final String vcfFileName, final int nfiles, final String suffix) throws IOException
{
if(nfiles > 1)
- return new File(vcfFileName+".filter");
+ return new File(vcfFileName+suffix);
final StickyFileChooser file_dialog = new StickyFileChooser();
- file_dialog.setSelectedFile(new File(vcfFileName+".filter"));
+ file_dialog.setSelectedFile(new File(vcfFileName+suffix));
file_dialog.setDialogTitle("Choose save file ...");
file_dialog.setDialogType(JFileChooser.SAVE_DIALOG);
final int status = file_dialog.showSaveDialog(null);
@@ -149,54 +146,60 @@ class IOUtils
final VCFview vcfView,
final boolean vcf_v4)
{
- // get all CDS features that do not have the /pseudo qualifier
+ // get all CDS features that do not have the /pseudo qualifier
final FeatureVector features = getFeatures(
new FeatureKeyQualifierPredicate(Key.CDS, "pseudo", false), entryGroup);
+ exportFasta(entryGroup, vcfReaders, chr, vcfView, vcf_v4, features);
+ }
+
+
+ protected static void exportFasta(final EntryGroup entryGroup,
+ final AbstractVCFReader vcfReaders[],
+ final String chr,
+ final VCFview vcfView,
+ final boolean vcf_v4,
+ final FeatureVector features)
+ {
+ String suffix = ".fasta";
+ if(features.size() == 1)
+ suffix = "."+features.elementAt(0).getIDString()+suffix;
for (int i = 0; i < vcfReaders.length; i++)
{
String vcfFileName = vcfReaders[i].getFileName();
try
{
- File filterFile = getFile(vcfFileName, vcfReaders.length);
+ File filterFile = getFile(vcfFileName, vcfReaders.length, suffix);
FileWriter writer = new FileWriter(filterFile);
for (int j = 0; j < features.size(); j++)
{
Feature f = features.elementAt(j);
FeatureSegmentVector segs = f.getSegments();
- Hashtable<String, String> seqs = new Hashtable<String, String>();
- String bases = f.getBases();
- seqs.put("ref", bases);
-
StringBuffer buff = new StringBuffer();
-
for(int k=0; k<segs.size(); k++)
{
FeatureSegment seg = segs.elementAt(k);
int sbeg = seg.getRawRange().getStart();
int send = seg.getRawRange().getEnd();
String segBases = seg.getBases();
-
+
if (vcfReaders[i] instanceof BCFReader)
{
BCFReaderIterator it = ((BCFReader) vcfReaders[i]).query(chr, sbeg, send);
- VCFRecord bcfRecord = null;
-
+ VCFRecord bcfRecord;
while ((bcfRecord = it.next()) != null)
- segBases = getSeqsVariations(bcfRecord, segBases, sbeg, f.isForwardFeature(), vcf_v4);
+ segBases = getSeqsVariation(bcfRecord, segBases, sbeg, f.isForwardFeature(), vcf_v4);
}
-
buff.append(segBases);
}
-
- Enumeration<String> en = seqs.keys();
- while(en.hasMoreElements())
- {
- String key = en.nextElement();
- bases = seqs.get(key);
- FastaStreamSequence stream = new FastaStreamSequence(bases, f.getIDString()+":"+key);
- stream.writeToStream(writer);
- }
+
+ StringBuffer header = new StringBuffer(f.getSystematicName());
+ header.append(" "+f.getIDString()+" ");
+ final String product = f.getProductString();
+ header.append( (product == null ? "undefined product" : product) );
+ header.append(" ").append(f.getWriteRange());
+
+ writeSequence(writer, header.toString(), buff.toString());
}
writer.close();
@@ -208,24 +211,23 @@ class IOUtils
}
}
- private static int getNumberOfDeletions(VCFRecord vcfRecord, boolean vcf_v4)
+ private static void writeSequence(FileWriter writer, String header, String bases) throws IOException
{
- if(vcf_v4)
- return vcfRecord.getRef().length()-vcfRecord.getAlt().length();
-
- int index = vcfRecord.getAlt().indexOf("D");
- int ndel = 0;
- try
+ writer.write (">" + header + "\n");
+
+ final int SEQUENCE_LINE_BASE_COUNT = 60;
+ for(int k=0; k<bases.length(); k+=SEQUENCE_LINE_BASE_COUNT)
{
- ndel = Integer.parseInt( vcfRecord.getAlt().substring(index+1) );
+ int end = k + SEQUENCE_LINE_BASE_COUNT;
+ if(end > bases.length())
+ end = bases.length();
+ writer.write ( bases.substring(k,end) + "\n");
}
- catch(NumberFormatException e) { e.printStackTrace(); }
- return ndel;
}
- protected static String getSeqsVariations(VCFRecord vcfRecord,
+ private static String getSeqsVariation(VCFRecord vcfRecord,
String bases, int sbeg, boolean isFwd, boolean vcf_v4)
- {
+ {
int position = vcfRecord.getPos()-sbeg;
if(!isFwd)
position = bases.length()-position;
@@ -233,24 +235,50 @@ class IOUtils
if(position > bases.length())
return bases;
- if(vcfRecord.isDeletion(vcf_v4))
+ StringBuffer buff = new StringBuffer();
+ if(isFwd)
+ buff.append(bases.substring(0,position));
+ else if(position > 0)
+ buff.append(bases.substring(0,position-1));
+
+ if(vcfRecord.getAlt().isDeletion(vcf_v4))
+ {
+ int ndel = vcfRecord.getAlt().getNumberOfDeletions(vcf_v4);
+ for(int i=0; i<ndel; i++)
+ buff.append("-");
+ position+=ndel;
+ }
+ else if(vcfRecord.getAlt().isInsertion(vcf_v4))
{
- int ndel = getNumberOfDeletions(vcfRecord, vcf_v4);
- if(isFwd)
- return bases.substring(0,position)+bases.substring(position+ndel);
- else
- return bases.substring(0,position-ndel)+bases.substring(position);
}
- else if(vcfRecord.isInsertion(vcf_v4))
+ else if(vcfRecord.getAlt().isMultiAllele())
{
+ }
+ else if(vcfRecord.getAlt().isNonVariant())
+ {
+ String ref = vcfRecord.getRef();
+ if(vcfRecord.getAlt().isNonVariant())
+ buff.append(ref.toUpperCase());
+ else
+ buff.append(ref);
}
else
{
-
+ String alt = vcfRecord.getAlt().toString();
+ if(vcfRecord.getAlt().isNonVariant())
+ buff.append(alt.toUpperCase());
+ else
+ buff.append(alt);
}
- return bases;
+
+ if(isFwd && position < bases.length())
+ buff.append(bases.substring(position+1));
+ else
+ buff.append(bases.substring(position));
+
+ return buff.toString();
}
/**
diff --git a/uk/ac/sanger/artemis/components/variant/VCFRecord.java b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
index 8427bb525000e9ab1092bdeb51d736497ed3aa0b..fcee2c9c48fb7d29d45629344a1d32f4fe354aee 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFRecord.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFRecord.java
@@ -23,6 +23,8 @@
package uk.ac.sanger.artemis.components.variant;
+import java.util.regex.Pattern;
+
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.io.Range;
@@ -36,13 +38,14 @@ class VCFRecord
private int pos;
private String ID;
private String ref;
- private String alt;
+ private VariantBase var;
private float quality;
private String filter;
private String info;
private String format;
private String data[][];
private short synFlag = -1;
+ protected static Pattern MULTI_ALLELE_PATTERN = Pattern.compile("^[AGCT]+,[AGCT,]+$");
/**
@@ -51,17 +54,10 @@ class VCFRecord
*/
public String toString()
{
- return chrom+"\t"+pos+"\t"+ID+"\t"+ref+"\t"+alt+"\t"+quality+
+ return chrom+"\t"+pos+"\t"+ID+"\t"+ref+"\t"+var.toString()+"\t"+quality+
"\t"+filter+"\t"+info+"\t"+format+"\t"+getSampleDataString();
}
-
- protected int getNumAlleles()
- {
- if (alt.equals("."))
- return 1;
-
- return alt.split(",").length+1;
- }
+
/**
* Parse a VCF line and return a VCFRecord
@@ -77,7 +73,7 @@ class VCFRecord
rec.pos = Integer.parseInt(parts[1]);
rec.ID = parts[2];
rec.ref = parts[3];
- rec.alt = parts[4];
+ rec.var = rec.new VariantBase(parts[4]);
try
{
@@ -211,9 +207,9 @@ class VCFRecord
/**
* @return the alt
*/
- protected String getAlt()
+ protected VariantBase getAlt()
{
- return alt;
+ return var;
}
/**
@@ -221,7 +217,7 @@ class VCFRecord
*/
protected void setAlt(String alt)
{
- this.alt = alt;
+ this.var = new VariantBase(alt);
}
/**
@@ -304,39 +300,7 @@ class VCFRecord
this.data = data;
}
- /**
- * Is this a deletion type.
- * @param variant
- * @return
- */
- protected boolean isDeletion(boolean vcf_v4)
- {
- if(vcf_v4)
- {
- if( alt.length() < ref.length() && !(alt.indexOf(",") > -1) )
- return true;
- }
- else if(alt.indexOf("D")>-1)
- return true;
- return false;
- }
-
- /**
- * Is this an insertion type.
- * @param variant
- * @return
- */
- protected boolean isInsertion(boolean vcf_v4)
- {
- if(vcf_v4)
- {
- if( alt.length() > ref.length() && !(alt.indexOf(",") > -1) )
- return true;
- }
- else if(alt.indexOf("I")>-1)
- return true;
- return false;
- }
+
/**
* @param features
@@ -363,7 +327,7 @@ class VCFRecord
*/
private short isSynonymous(FeatureVector features, int basePosition)
{
- char variant = getAlt().toLowerCase().charAt(0);
+ char variant = getAlt().toString().toLowerCase().charAt(0);
int intronlength = 0;
Range lastRange = null;
@@ -450,4 +414,95 @@ class VCFRecord
return 3;
}
+ public class VariantBase
+ {
+ private String alt;
+ public VariantBase(String alt)
+ {
+ this.alt = alt;
+ }
+
+ public String toString()
+ {
+ return alt;
+ }
+
+ protected int length()
+ {
+ return alt.length();
+ }
+
+ /**
+ * Is this a deletion type.
+ * @param variant
+ * @return
+ */
+ protected boolean isDeletion(boolean vcf_v4)
+ {
+ if(vcf_v4)
+ {
+ if( alt.length() < ref.length() && !(alt.indexOf(",") > -1) )
+ return true;
+ }
+ else if(alt.indexOf("D")>-1)
+ return true;
+ return false;
+ }
+
+ /**
+ * Is this an insertion type.
+ * @param variant
+ * @return
+ */
+ protected boolean isInsertion(boolean vcf_v4)
+ {
+ if(vcf_v4)
+ {
+ if( alt.length() > ref.length() && !(alt.indexOf(",") > -1) )
+ return true;
+ }
+ else if(alt.indexOf("I")>-1)
+ return true;
+ return false;
+ }
+
+ protected boolean isMultiAllele()
+ {
+ if(VCFRecord.MULTI_ALLELE_PATTERN.matcher(alt).matches())
+ return true;
+ return false;
+ }
+
+ protected int getNumAlleles()
+ {
+ if (alt.equals("."))
+ return 1;
+
+ return alt.split(",").length+1;
+ }
+
+ protected int getNumberOfDeletions(boolean vcf_v4)
+ {
+ String alt = getAlt().toString();
+ if(vcf_v4)
+ return getRef().length()-alt.length();
+
+ int index = alt.indexOf("D");
+ int ndel = 0;
+ try
+ {
+ ndel = Integer.parseInt( alt.substring(index+1) );
+ }
+ catch(NumberFormatException e) { e.printStackTrace(); }
+ return ndel;
+ }
+
+ protected boolean isNonVariant()
+ {
+ if(alt.equals("."))
+ return true;
+ return false;
+ }
+ }
+
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index e4f18a0235469cc1d394590c3f8a42e5e7e299ff..f8b7414f2c7e0c1282928f4b51606a960497181d 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -52,7 +52,6 @@ import java.net.URL;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
-import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.swing.ButtonGroup;
@@ -160,8 +159,6 @@ public class VCFview extends JPanel
Hashtable<String, Integer> offsetLengths = null;
private boolean concatSequences = false;
-
- private Pattern multiAllelePattern = Pattern.compile("^[AGCT]+,[AGCT,]+$");
protected static Pattern tabPattern = Pattern.compile("\t");
public static String VCFFILE_SUFFIX = ".*\\.[bv]{1}cf(\\.gz)*$";
@@ -186,7 +183,7 @@ public class VCFview extends JPanel
this.feature_display = feature_display;
this.vcfPanel = vcfPanel;
this.vcfFiles = vcfFiles;
-
+
setBackground(Color.white);
MultiLineToolTipUI.initialize();
setToolTipText("");
@@ -514,6 +511,18 @@ public class VCFview extends JPanel
});
export.add(exportVCF);
+ final JMenuItem exportFastaSelected = new JMenuItem("Export FASTA of selected features");
+ exportFastaSelected.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e)
+ {
+ VCFview.this.setCursor(new Cursor(Cursor.WAIT_CURSOR));
+ IOUtils.exportFasta(entryGroup, vcfReaders, chr, VCFview.this, vcf_v4,
+ selection.getAllFeatures());
+ VCFview.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
+ }
+ });
+ export.add(exportFastaSelected);
+
final JMenuItem exportFasta = new JMenuItem("Export FASTA");
exportFasta.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e)
@@ -919,10 +928,10 @@ public class VCFview extends JPanel
protected boolean showVariant(VCFRecord record, FeatureVector features, int basePosition)
{
- if(!showDeletions && record.isDeletion(vcf_v4))
+ if(!showDeletions && record.getAlt().isDeletion(vcf_v4))
return false;
- if(!showInsertions && record.isInsertion(vcf_v4))
+ if(!showInsertions && record.getAlt().isInsertion(vcf_v4))
return false;
if(!VCFFilter.passFilter(record))
@@ -931,14 +940,14 @@ public class VCFview extends JPanel
if(!showNonOverlappings && !isOverlappingFeature(features, basePosition))
return false;
- if(!showNonVariants && record.getAlt().equals("."))
+ if(!showNonVariants && record.getAlt().isNonVariant())
return false;
short isSyn = -1;
markAsNewStop = false;
if(markNewStops.isSelected() &&
- !record.isDeletion(vcf_v4) &&
- !record.isInsertion(vcf_v4) &&
+ !record.getAlt().isDeletion(vcf_v4) &&
+ !record.getAlt().isInsertion(vcf_v4) &&
record.getAlt().length() == 1 &&
record.getRef().length() == 1)
{
@@ -948,8 +957,8 @@ public class VCFview extends JPanel
}
if( (!showSynonymous || !showNonSynonymous) &&
- !record.isDeletion(vcf_v4) &&
- !record.isInsertion(vcf_v4) &&
+ !record.getAlt().isDeletion(vcf_v4) &&
+ !record.getAlt().isInsertion(vcf_v4) &&
record.getAlt().length() == 1 &&
record.getRef().length() == 1)
{
@@ -961,7 +970,7 @@ public class VCFview extends JPanel
return false;
}
- if(!showMultiAlleles && multiAllelePattern.matcher(record.getAlt()).matches())
+ if(!showMultiAlleles && record.getAlt().isMultiAllele())
return false;
return true;
@@ -1000,16 +1009,15 @@ public class VCFview extends JPanel
g.setColor(getQualityColour(record));
else
{
- if(record.isDeletion(vcf_v4))
+ if(record.getAlt().isDeletion(vcf_v4))
g.setColor(Color.gray);
- else if(record.isInsertion(vcf_v4))
+ else if(record.getAlt().isInsertion(vcf_v4))
g.setColor(Color.yellow);
else if(record.getAlt().length() == 1 && record.getRef().length() == 1)
g.setColor(getColourForSNP(record, features, basePosition));
else
{
- Matcher m = multiAllelePattern.matcher(record.getAlt());
- if(m.matches())
+ if(record.getAlt().isMultiAllele())
{
g.setColor(Color.orange);
g.fillArc(pos[0]-3, pos[1]-LINE_HEIGHT-3, 6, 6, 0, 360);
@@ -1035,7 +1043,7 @@ public class VCFview extends JPanel
private Color getColourForSNP(VCFRecord record, FeatureVector features, int basePosition)
{
if(colourScheme == VARIANT_COLOUR_SCHEME)
- return getVariantColour(record.getAlt());
+ return getVariantColour(record.getAlt().toString());
else if(colourScheme == SYN_COLOUR_SCHEME) // synonymous / non-synonymous
{
short synFlag = record.getSynFlag(features, basePosition);
@@ -1044,7 +1052,7 @@ public class VCFview extends JPanel
else if(synFlag == 0 || synFlag == 2)
return Color.blue;
else
- return getVariantColour(record.getAlt());
+ return getVariantColour(record.getAlt().toString());
}
else // score
return getQualityColour(record);