VcfBurdenFilterGenes.java

/*
The MIT License (MIT)

Copyright (c) 2014 Pierre Lindenbaum

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.


History:

*/
package com.github.lindenb.jvarkit.tools.burden;

import java.io.File;
import java.nio.file.Files;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;

import htsjdk.samtools.util.CloserUtil;
import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import htsjdk.variant.variantcontext.writer.VariantContextWriter;
import htsjdk.variant.vcf.VCFFilterHeaderLine;
import htsjdk.variant.vcf.VCFHeader;

import com.github.lindenb.jvarkit.util.picard.SAMSequenceDictionaryProgress;
import com.github.lindenb.jvarkit.util.vcf.VcfIterator;
import com.github.lindenb.jvarkit.util.vcf.predictions.VepPredictionParser;
import com.github.lindenb.jvarkit.util.vcf.predictions.VepPredictionParserFactory;

import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.util.jcommander.Launcher;
import com.github.lindenb.jvarkit.util.jcommander.Program;
import com.github.lindenb.jvarkit.util.log.Logger;
/**

BEGIN_DOC

### Example

```
echo "IL2" > genes.txt
 echo "NOCTH2" >>  genes.txt
 gunzip -c inputx.vcf.gz |\
 java -jar dit/vcfburdenfiltergenes.jar -g genes.txt
```



END_DOC
*/
@Program(
		name="vcfburdenfiltergenes",
		description="Filter VEP Output from a list of genes.",
		keywords={"gene","vcf","vep"})
public class VcfBurdenFilterGenes
	extends Launcher
	{
	private static final Logger LOG = Logger.build(VcfBurdenFilterGenes.class).make();

	@Parameter(names={"-o","--output"},description="Output file. Optional . Default: stdout")
	private File outputFile = null;


	@Parameter(names={"-g","--genes"},description="Gene file: one name per line")
	private File geneFile = null;

	@Parameter(names={"-filter","--filter"},description="If empty: remove the variants from the VCF. If not empty, add a token in the column filter.")
	private String filterTag = "";

	private final Set<String> geneNames= new HashSet<>();
	
	
	
	public VcfBurdenFilterGenes()
		{
		}
	
	@Override
	protected int doVcfToVcf(
			final String inputName,
			final VcfIterator in,
			final VariantContextWriter out
			) 
		{
		final VCFHeader header=in.getHeader();		
		try {
			final VCFHeader h2=addMetaData(new VCFHeader(header));

			final VCFFilterHeaderLine filterControlsHeader;
			if(!this.filterTag.trim().isEmpty())
				{
				filterControlsHeader = new VCFFilterHeaderLine(
						this.filterTag.trim(),
						"Genes in list "+this.filterTag
						);
				h2.addMetaDataLine(filterControlsHeader);
				}
			else
				{
				filterControlsHeader = null;
				}
			final List<String> lookColumns=Arrays.asList(
					"CCDS",
					"Feature",
					"ENSP",
					"Gene",
					"HGNC",
					"HGNC_ID",					
					"SYMBOL",					
					"RefSeq"					
					);
			final VepPredictionParser vepParser = new VepPredictionParserFactory(header).get();
			final SAMSequenceDictionaryProgress progess=new SAMSequenceDictionaryProgress(header.getSequenceDictionary());
			out.writeHeader(h2);
			while(in.hasNext() &&  !out.checkError())
				{
				final VariantContext ctx = progess.watch(in.next());
				boolean keep=false;
				final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
				
				
				final List<String> csqList= ctx.getAttributeAsList(vepParser.getTag()).stream().
						map(O->String.class.cast(O)).collect(Collectors.toList());
				
				//not just set FILTER ?
				if(filterControlsHeader==null) {
					vcb.rmAttribute(vepParser.getTag());
				}
				
				final List<String> newCsqList=new ArrayList<>();
				for(final String predStr: csqList) {
					final VepPredictionParser.VepPrediction pred = vepParser.parseOnePrediction(ctx,predStr);
					for(final String col:lookColumns) {
						final String token = pred.getByCol(col);
						if(token!=null && !token.isEmpty() && this.geneNames.contains(token))
							{
							newCsqList.add(predStr);
							keep=true;
							break;
							}
						}
					}
				//not just set FILTER ?
				if(filterControlsHeader==null) {
					vcb.attribute(vepParser.getTag(),newCsqList);
				}
				
				
				if(filterControlsHeader!=null)
					{
					if(!keep) vcb.filter(filterControlsHeader.getID());
					out.add(ctx);
					}
				else
					{
					if(keep) out.add(vcb.make());
					}
				}
			progess.finish();
			return RETURN_OK;
			} catch(final Exception err) {
				LOG.error(err);
				return -1;
			} finally {
				CloserUtil.close(in);
			}
		}
	
	 	
	@Override
	public int doWork(final List<String> args) {
		if(this.geneFile==null || !this.geneFile.exists()) {
			LOG.error("Undefined gene file option.");
			return -1;
			}
			
		try {
			this.geneNames.clear();
			this.geneNames.addAll(Files.readAllLines(this.geneFile.toPath()));
			geneNames.remove(".");
			geneNames.remove("");
			LOG.info("number of genes : "+geneNames.size());
			return doVcfToVcf(args,outputFile);
		} catch (final Exception err) {
			LOG.error(err);
			return -1;
			}
		}
	
	public static void main(String[] args)
		{
		new VcfBurdenFilterGenes().instanceMainWithExit(args);
		}
	}