@Override
public int doWork(String[] args) {
com.github.lindenb.jvarkit.util.cli.GetOpt opt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
while ((c = opt.getopt(args, getGetOptDefault() + "f:A:Svdo:")) != -1) {
switch (c) {
case 'o':
this.setOutputFile(new File(opt.getOptArg()));
break;
case 'd':
this.setReasoning(false);
break;
case 'v':
this.setInverseResult(true);
break;
case 'S':
{
for (SequenceOntologyTree.Term t : sequenceOntologyTree.getTerms()) {
System.out.println(t.getAcn() + "\t" + t.getLabel());
}
return 0;
}
case 'A':
{
this.addTerm(opt.getOptArg().trim());
break;
}
case 'f':
{
try {
parseAccessionsFile(new File(opt.getOptArg()));
} catch (IOException err) {
error(err);
return -1;
}
break;
}
default:
{
switch (handleOtherOptions(c, opt, args)) {
case EXIT_FAILURE:
return -1;
case EXIT_SUCCESS:
return 0;
default:
break;
}
}
}
}
return mainWork(opt.getOptInd(), args);
}
@Override
public int initializeKnime() {
for (String acn : this.userTermsAsString) {
acn = acn.trim();
if (acn.isEmpty()) continue;
SequenceOntologyTree.Term t = sequenceOntologyTree.getTermByAcn(acn);
if (t == null) {
error("Unknown SO:Accession \"" + acn + "\"");
return -1;
}
this.user_terms.add(t);
if (reasoning) this.user_terms.addAll(t.getAllDescendants());
}
if (this.user_terms.isEmpty()) {
warning("No SO: term found ");
}
info("Will be using :" + this.user_terms.toString());
this.userTermsAsString = null; // we don't need this anymore
return super.initializeKnime();
}
/**
* VCF filter on Sequence Ontology
*
* @author lindenb
*/
public class VcfFilterSequenceOntology extends AbstractVCFFilter3 {
private Set<String> userTermsAsString = new HashSet<String>();
/* enable reasoning */
private boolean reasoning = true;
/* all sequence terms */
private Set<SequenceOntologyTree.Term> user_terms = new HashSet<SequenceOntologyTree.Term>();
/* inverse result */
private boolean inverse_result = false;
private final SequenceOntologyTree sequenceOntologyTree = SequenceOntologyTree.getInstance();
/* public : knime needs this*/
public VcfFilterSequenceOntology() {}
@Override
public String getProgramDescription() {
return "Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology."
+ " Reasoning : Children of user's SO-terms will be also used.";
}
@Override
protected String getOnlineDocUrl() {
return DEFAULT_WIKI_PREFIX + "VcfFilterSequenceOntology";
}
private boolean hasUserTem(Set<SequenceOntologyTree.Term> ctxTerms) {
for (SequenceOntologyTree.Term ctxTerm : ctxTerms) {
if (this.user_terms.contains(ctxTerm)) {
return true;
}
}
return false;
}
@Override
protected void doWork(String source, VcfIterator in, VariantContextWriter out)
throws IOException {
try {
VCFHeader header = in.getHeader();
VCFHeader h2 = new VCFHeader(header);
h2.addMetaDataLine(
new VCFHeaderLine(
getClass().getSimpleName() + "CmdLine", String.valueOf(getProgramCommandLine())));
h2.addMetaDataLine(
new VCFHeaderLine(getClass().getSimpleName() + "Version", String.valueOf(getVersion())));
h2.addMetaDataLine(
new VCFHeaderLine(
getClass().getSimpleName() + "HtsJdkVersion", HtsjdkVersion.getVersion()));
h2.addMetaDataLine(
new VCFHeaderLine(getClass().getSimpleName() + "HtsJdkHome", HtsjdkVersion.getHome()));
out.writeHeader(h2);
final VepPredictionParser vepParser = new VepPredictionParser(header);
final SnpEffPredictionParser snpEffparser = new SnpEffPredictionParser(header);
final MyPredictionParser myPredParser = new MyPredictionParser(header);
SAMSequenceDictionaryProgress progress =
new SAMSequenceDictionaryProgress(header.getSequenceDictionary());
while (in.hasNext()) {
this.checkKnimeCancelled();
VariantContext ctx = progress.watch(in.next());
boolean keep = false;
for (SnpEffPredictionParser.SnpEffPrediction pred : snpEffparser.getPredictions(ctx)) {
if (hasUserTem(pred.getSOTerms())) {
keep = true;
break;
}
}
if (!keep) {
for (VepPredictionParser.VepPrediction pred : vepParser.getPredictions(ctx)) {
if (hasUserTem(pred.getSOTerms())) {
keep = true;
break;
}
}
}
if (!keep) {
for (MyPredictionParser.MyPrediction pred : myPredParser.getPredictions(ctx)) {
if (hasUserTem(pred.getSOTerms())) {
keep = true;
break;
}
}
}
if (isInverseResult()) keep = !keep;
if (keep) {
incrVariantCount();
out.add(ctx);
}
if (checkOutputError()) break;
}
progress.finish();
} finally {
}
}
@Override
public void printOptions(PrintStream out) {
out.println(" -A (SO:ACN). add this SO:ACN");
out.println(" -f (filename). Tab delimited file of SO accession numbers");
out.println(" -S list the available SO accession and exit.");
out.println(" -v invert selection.");
out.println(" -d disable reasoning, don't use term's children.");
super.printOptions(out);
}
private void parseAccessionsFile(File f) throws IOException {
BufferedReader in = IOUtils.openFileForBufferedReading(f);
String line;
while ((line = in.readLine()) != null) {
if (line.startsWith("#")) continue;
line = line.trim();
if (line.trim().isEmpty()) continue;
addTerm(line);
}
in.close();
}
@Override
public int initializeKnime() {
for (String acn : this.userTermsAsString) {
acn = acn.trim();
if (acn.isEmpty()) continue;
SequenceOntologyTree.Term t = sequenceOntologyTree.getTermByAcn(acn);
if (t == null) {
error("Unknown SO:Accession \"" + acn + "\"");
return -1;
}
this.user_terms.add(t);
if (reasoning) this.user_terms.addAll(t.getAllDescendants());
}
if (this.user_terms.isEmpty()) {
warning("No SO: term found ");
}
info("Will be using :" + this.user_terms.toString());
this.userTermsAsString = null; // we don't need this anymore
return super.initializeKnime();
}
public void addTerm(String acn) {
this.userTermsAsString.add(acn);
}
public void setReasoning(boolean reasoning) {
this.reasoning = reasoning;
}
public boolean isReasoning() {
return reasoning;
}
public boolean isInverseResult() {
return inverse_result;
}
public void setInverseResult(boolean inverse_result) {
this.inverse_result = inverse_result;
}
@Override
public int doWork(String[] args) {
com.github.lindenb.jvarkit.util.cli.GetOpt opt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
while ((c = opt.getopt(args, getGetOptDefault() + "f:A:Svdo:")) != -1) {
switch (c) {
case 'o':
this.setOutputFile(new File(opt.getOptArg()));
break;
case 'd':
this.setReasoning(false);
break;
case 'v':
this.setInverseResult(true);
break;
case 'S':
{
for (SequenceOntologyTree.Term t : sequenceOntologyTree.getTerms()) {
System.out.println(t.getAcn() + "\t" + t.getLabel());
}
return 0;
}
case 'A':
{
this.addTerm(opt.getOptArg().trim());
break;
}
case 'f':
{
try {
parseAccessionsFile(new File(opt.getOptArg()));
} catch (IOException err) {
error(err);
return -1;
}
break;
}
default:
{
switch (handleOtherOptions(c, opt, args)) {
case EXIT_FAILURE:
return -1;
case EXIT_SUCCESS:
return 0;
default:
break;
}
}
}
}
return mainWork(opt.getOptInd(), args);
}
public static void main(String[] args) {
new VcfFilterSequenceOntology().instanceMainWithExit(args);
}
}