From d99d0678b433be01c67386c7cccf8e7d56a517e6 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 8 Feb 2012 16:33:39 +0000
Subject: [PATCH] changes to writing variant sites
---
.../artemis/components/variant/IOUtils.java | 67 +++++++++++++++----
1 file changed, 54 insertions(+), 13 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java
index 0a2765e03..ec1d7a8af 100644
--- a/uk/ac/sanger/artemis/components/variant/IOUtils.java
+++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java
@@ -179,10 +179,6 @@ class IOUtils
protected static void exportVariantFasta(final VCFview vcfView)
{
final EntryGroup entryGroup = vcfView.getEntryGroup();
- int length = entryGroup.getSequenceLength();
- final Bases bases = entryGroup.getBases();
- final FeatureVector features = entryGroup.getAllFeatures();
-
final String name = entryGroup.getActiveEntries().elementAt(0).getName();
final File newfile = new File(
getBaseDirectoryFromEntry(entryGroup.getActiveEntries().elementAt(0)),
@@ -194,6 +190,30 @@ class IOUtils
if(f == null)
return;
+ exportVariantFasta(vcfView,
+ new PrintWriter(new FileOutputStream(f)),
+ entryGroup.getSequenceLength(),
+ entryGroup.getAllFeatures(),
+ entryGroup.getBases());
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ }
+ }
+
+ /**
+ * Export all variant sites to a multiple fasta file.
+ * @param vcfView
+ */
+ protected static void exportVariantFasta(final VCFview vcfView,
+ final PrintWriter pw,
+ final int length,
+ final FeatureVector features,
+ final Bases bases)
+ {
+ try
+ {
int ntotalSamples = 0;
for (int i = 0; i < vcfView.getVcfReaders().length; i++)
ntotalSamples += vcfView.getVcfReaders()[i].getNumberOfSamples();
@@ -206,16 +226,18 @@ class IOUtils
final String names[] = vcfView.getVcfReaders()[i].sampleNames;
for(int j=0; j<names.length; j++)
{
- tmpFiles[i+j] = File.createTempFile(names[j].replaceAll("[/\\:]", "_"), "art");
+ final String fn = (names[j].equals("") ? (j+1)+"_sample" : names[j].replaceAll("[/\\:]", "_"));
+ tmpFiles[i+j] = File.createTempFile(fn, "art");
writer[i+j] = new FileWriter( tmpFiles[i+j] );
- writer[i+j].write(">"+names[j]);
+ writer[i+j].write(">"+fn);
}
}
// include reference bases
+ final String refName = vcfView.getEntryGroup().getActiveEntries().elementAt(0).getName();
tmpFiles[ntotalSamples] = File.createTempFile("ref", "art");
writer[ntotalSamples] = new FileWriter( tmpFiles[ntotalSamples] );
- writer[ntotalSamples].write(">reference");
+ writer[ntotalSamples].write(">"+refName);
final int MAX_BASE_CHUNK = (10000/ntotalSamples)*SEQUENCE_LINE_BASE_COUNT;
@@ -223,7 +245,6 @@ class IOUtils
int baseCount = 0;
// write variant sites to tmp files
- //length = 2172095;
for(int i=0; i<length; i+=MAX_BASE_CHUNK)
{
int start = i+1;
@@ -240,7 +261,6 @@ class IOUtils
writer[i].close();
// concatenate the single fasta files into a multiple fasta file
- final PrintWriter pw = new PrintWriter(new FileOutputStream(f));
for (int i = 0; i < tmpFiles.length; i++)
{
final BufferedReader br = new BufferedReader(new FileReader(tmpFiles[i].getPath()));
@@ -367,8 +387,7 @@ class IOUtils
if(record == null)
continue;
-
-
+
boolean vcf_v4 = reader.isVcf_v4();
int nsamples = reader.getNumberOfSamples();
// loop over each sample
@@ -379,7 +398,22 @@ class IOUtils
{
if(record.getAlt().isDeletion(vcf_v4))
{
+ // note: do not write out if just deletion
thisBase[thisSample] = "-";
+
+ /*if( thisBase[ntotalSamples] == null ||
+ thisBase[ntotalSamples].length() < record.getRef().length() )
+ {
+ thisBase[ntotalSamples] = record.getRef();
+ if(!record.getAlt().toString().equals("."))
+ thisBase[thisSample] = record.getAlt().toString();
+ else
+ thisBase[thisSample] = "";
+
+ int padLength = thisBase[ntotalSamples].length() - thisBase[thisSample].length();
+ for(int ipad=0; ipad<padLength; ipad++)
+ thisBase[thisSample] += "-";
+ }*/
}
else if(record.getAlt().isInsertion(vcf_v4))
{
@@ -389,6 +423,12 @@ class IOUtils
thisBase[thisSample] = in;
if(in.length() > insertionLength)
insertionLength = in.length();
+ seenSNP = true;
+
+ if( (thisBase[ntotalSamples] == null ||
+ thisBase[ntotalSamples].length() < record.getRef().length()) &&
+ in.toLowerCase().startsWith(record.getRef().toLowerCase()))
+ thisBase[ntotalSamples] = record.getRef();
}
else if(record.getAlt().isMultiAllele(k))
{
@@ -400,11 +440,12 @@ class IOUtils
}
}
else if(record.getAlt().isNonVariant())
+ {
thisBase[thisSample] = ".";
+ }
else
{
- if(record.getAlt().toString().length() > 1 &&
- record.getAlt().toString().length() == record.getRef().length() )
+ if(record.getAlt().toString().length() == record.getRef().length() )
{
thisBase[thisSample] = record.getAlt().toString();
seenSNP = true;
--
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