/**
* Calculate snp effect for a list of snps
*
* @param snpEffFile
*/
public void snpEffect(String vcfFile, String txtFile, String aaHgsv, String genotype) {
// Create command
String argsVcf[] = {"-classic", "-cancer", "-hgvs", "testHg3766Chr1", vcfFile};
String argsTxt[] = {
"-classic", "-cancer", "-cancerSamples", txtFile, "-hgvs", "testHg3766Chr1", vcfFile
};
String args[] = (txtFile == null ? argsVcf : argsTxt);
SnpEff cmd = new SnpEff(args);
SnpEffCmdEff cmdEff = (SnpEffCmdEff) cmd.snpEffCmd();
// Run command
List<VcfEntry> list = cmdEff.run(true);
// Find AA change for a genotype
boolean found = false;
for (VcfEntry vcfEntry : list) {
for (VcfEffect eff : vcfEntry.parseEffects()) {
if (genotype.equals(eff.getGenotype())) {
if (debug) Gpr.debug("AA: " + eff.getAa() + "\t" + eff.getGenotype() + "\t" + eff);
Assert.assertEquals(aaHgsv, eff.getAa());
found = true;
}
}
}
// Not found? Error
if (!found) throw new RuntimeException("Genotype '" + genotype + "' not found.");
}
/** Add some lines to header before showing it */
@Override
public boolean addHeaders(VcfFileIterator vcfFile) {
super.addHeaders(vcfFile);
for (String key : fieldsToAdd.keySet()) {
// Get type
String type = fieldsType.get(key);
if (type == null) {
System.err.println("WARNING: Cannot find type for field '" + key + "', using 'String'.");
type = VcfInfoType.String.toString();
}
String infoKey = VcfEntry.vcfInfoKeySafe(DBNSFP_VCF_INFO_PREFIX + key);
vcfFile
.getVcfHeader()
.addLine(
"##INFO=<ID="
+ infoKey
+ ",Number=A,Type="
+ type
+ ",Description=\""
+ fieldsToAdd.get(key)
+ "\">");
}
return false;
}
@Override
public boolean annotate(VcfEntry vcfEntry) {
boolean annotated = false;
Map<String, String> info = new HashMap<>();
// Find annotations for each variant in this VcfEntry
for (Variant var : vcfEntry.variants()) annotated |= annotate(var, info);
// Add annotations to VcfEntry
if (annotated) {
// Sort keys and add them to VcfEntry
ArrayList<String> keys = new ArrayList<>();
keys.addAll(info.keySet());
Collections.sort(keys);
// Add INFO fields
for (String key : keys) {
String infoKey = VcfEntry.vcfInfoKeySafe(DBNSFP_VCF_INFO_PREFIX + key);
vcfEntry.addInfo(infoKey, info.get(key));
}
}
return annotated;
}
/** Annotate a VCF file using dbNSFP */
ArrayList<VcfEntry> annotate(boolean createList) {
ArrayList<VcfEntry> list = (createList ? new ArrayList<VcfEntry>() : null);
// Open VCF file
vcfFile = new VcfFileIterator(vcfFileName);
vcfFile.setDebug(debug);
// Initialize annotations
try {
annotateInit(vcfFile);
} catch (Exception e) {
throw new RuntimeException(e);
}
// Annotate VCF file
if (verbose) Timer.showStdErr("Annotating file '" + vcfFileName + "'");
boolean showHeader = true;
int pos = -1;
String chr = "";
for (VcfEntry vcfEntry : vcfFile) {
try {
// Show header?
if (showHeader) {
// Add VCF header
addHeaders(vcfFile);
String headerStr = vcfFile.getVcfHeader().toString();
if (!headerStr.isEmpty()) print(headerStr);
showHeader = false;
// Check that the fields we want to add are actually in the database
checkFieldsToAdd();
}
// Check if file is sorted
if (vcfEntry.getChromosomeName().equals(chr) && vcfEntry.getStart() < pos) {
fatalError(
"Your VCF file should be sorted!" //
+ "\n\tPrevious entry "
+ chr
+ ":"
+ pos //
+ "\n\tCurrent entry "
+ vcfEntry.getChromosomeName()
+ ":"
+ (vcfEntry.getStart() + 1) //
);
}
// Annotate
annotate(vcfEntry);
// Show
print(vcfEntry);
if (list != null) list.add(vcfEntry);
count++;
// Update chr:pos
chr = vcfEntry.getChromosomeName();
pos = vcfEntry.getStart();
} catch (IOException e) {
throw new RuntimeException(e);
}
}
annotateFinish();
vcfFile.close();
// Show some stats
if (verbose) {
double perc = (100.0 * countAnnotated) / count;
Timer.showStdErr(
"Done." //
+ "\n\tTotal annotated entries : "
+ countAnnotated //
+ "\n\tTotal entries : "
+ count //
+ "\n\tPercent : "
+ String.format("%.2f%%", perc) //
);
}
return list;
}