VcfEigen01.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:

* 2016 creation

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


import java.io.File;
import java.util.List;
import java.util.Map;

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

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.VCFHeader;
import htsjdk.variant.vcf.VCFInfoHeaderLine;


/**

BEGIN_DOC


Annotate a VCF with the Eigen data ( http://www.columbia.edu/~ii2135/eigen.html)



### About Eigen

"Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as made available by the ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike most existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations. We show that the resulting meta-score has good discriminatory ability using disease associated and putatively benign variants from published studies (for both Mendelian and complex diseases). The Eigen score is particularly useful in prioritizing likely causal variants in a region of interest when it is combined with population-level genetic data in the framework of a hierarchical model. Furthermore, an important advantage of the Eigen score is that it can be easily adapted to a specific tissue or cell type. More information about the Eigen score can be found in the accompanying manuscript: A spectral approach integrating functional genomic annotations for coding and noncoding variants (Iuliana Ionita-Laza, Kenneth McCallum, Bin Xu, Joseph Buxbaum). 


### Example



```

$ gunzip -c input.vcf.gz | cut -f 1-8 | java -jar dist/vcfeigen01.jar -D eigen_data_dir  | grep -i eigen

##INFO=<ID=EIGEN_CODING_Consequence,Number=A,Type=String,Description="Consequence">
##INFO=<ID=EIGEN_CODING_Eigen_PC_phred,Number=A,Type=Float,Description="Eigen-PC-phred">
##INFO=<ID=EIGEN_CODING_Eigen_PC_raw,Number=A,Type=Float,Description="Eigen-PC-raw">
##INFO=<ID=EIGEN_CODING_Eigen_phred,Number=A,Type=Float,Description="Eigen-phred">
##INFO=<ID=EIGEN_CODING_Eigen_raw,Number=A,Type=Float,Description="Eigen-raw">
##INFO=<ID=EIGEN_CODING_GERP_NR,Number=A,Type=Float,Description="GERP_NR">
##INFO=<ID=EIGEN_CODING_GERP_RS,Number=A,Type=Float,Description="GERP_RS">
##INFO=<ID=EIGEN_CODING_MA,Number=A,Type=Float,Description="MA">
##INFO=<ID=EIGEN_CODING_PhastPla,Number=A,Type=Float,Description="PhastPla">
##INFO=<ID=EIGEN_CODING_PhastPri,Number=A,Type=Float,Description="PhastPri">
##INFO=<ID=EIGEN_CODING_PhastVer,Number=A,Type=Float,Description="PhastVer">
##INFO=<ID=EIGEN_CODING_PhyloPla,Number=A,Type=Float,Description="PhyloPla">
##INFO=<ID=EIGEN_CODING_PhyloPri,Number=A,Type=Float,Description="PhyloPri">
##INFO=<ID=EIGEN_CODING_PhyloVer,Number=A,Type=Float,Description="PhyloVer">
##INFO=<ID=EIGEN_CODING_PolyPhenDIV,Number=A,Type=Float,Description="PolyPhenDIV">
##INFO=<ID=EIGEN_CODING_PolyPhenVar,Number=A,Type=Float,Description="PolyPhenVar">
##INFO=<ID=EIGEN_CODING_SIFT,Number=A,Type=Float,Description="SIFT">
##INFO=<ID=EIGEN_NC_DnasePval,Number=A,Type=Float,Description="DnasePval">
##INFO=<ID=EIGEN_NC_DnaseSig,Number=A,Type=Float,Description="DnaseSig">
##INFO=<ID=EIGEN_NC_Eigen_PC_phred,Number=A,Type=Float,Description="Eigen-PC-phred">
##INFO=<ID=EIGEN_NC_Eigen_PC_raw,Number=A,Type=Float,Description="Eigen-PC-raw">
##INFO=<ID=EIGEN_NC_Eigen_phred,Number=A,Type=Float,Description="Eigen-phred">
##INFO=<ID=EIGEN_NC_Eigen_raw,Number=A,Type=Float,Description="Eigen-raw">
##INFO=<ID=EIGEN_NC_FairePval,Number=A,Type=Float,Description="FairePval">
##INFO=<ID=EIGEN_NC_FaireSig,Number=A,Type=Float,Description="FaireSig">
##INFO=<ID=EIGEN_NC_GERP_NR,Number=A,Type=Float,Description="GERP_NR">
##INFO=<ID=EIGEN_NC_GERP_RS,Number=A,Type=Float,Description="GERP_RS">
##INFO=<ID=EIGEN_NC_H3K27ac,Number=A,Type=Float,Description="H3K27ac">
##INFO=<ID=EIGEN_NC_H3K4Me1,Number=A,Type=Float,Description="H3K4Me1">
##INFO=<ID=EIGEN_NC_H3K4Me3,Number=A,Type=Float,Description="H3K4Me3">
##INFO=<ID=EIGEN_NC_OCPval,Number=A,Type=Float,Description="OCPval">
##INFO=<ID=EIGEN_NC_PhastPla,Number=A,Type=Float,Description="PhastPla">
##INFO=<ID=EIGEN_NC_PhastPri,Number=A,Type=Float,Description="PhastPri">
##INFO=<ID=EIGEN_NC_PhastVer,Number=A,Type=Float,Description="PhastVer">
##INFO=<ID=EIGEN_NC_PhyloPla,Number=A,Type=Float,Description="PhyloPla">
##INFO=<ID=EIGEN_NC_PhyloPri,Number=A,Type=Float,Description="PhyloPri">
##INFO=<ID=EIGEN_NC_PhyloVer,Number=A,Type=Float,Description="PhyloVer">
##INFO=<ID=EIGEN_NC_PolIIPval,Number=A,Type=Float,Description="PolIIPval">
##INFO=<ID=EIGEN_NC_PolIISig,Number=A,Type=Float,Description="PolIISig">
##INFO=<ID=EIGEN_NC_TFBS_max,Number=A,Type=Float,Description="TFBS_max">
##INFO=<ID=EIGEN_NC_TFBS_num,Number=A,Type=Float,Description="TFBS_num">
##INFO=<ID=EIGEN_NC_TFBS_sum,Number=A,Type=Float,Description="TFBS_sum">
##INFO=<ID=EIGEN_NC_cmycPval,Number=A,Type=Float,Description="cmycPval">
##INFO=<ID=EIGEN_NC_cmycSig,Number=A,Type=Float,Description="cmycSig">
##INFO=<ID=EIGEN_NC_ctcfPval,Number=A,Type=Float,Description="ctcfPval">
##INFO=<ID=EIGEN_NC_ctcfSig,Number=A,Type=Float,Description="ctcfSig">
(...)
14	741	.	A	C	1	.	EIGEN_NC_DnasePval=0.0;EIGEN_NC_DnaseSig=0.0;EIGEN_NC_Eigen_PC_phred=7.69892;EIGEN_NC_Eigen_PC_raw=-0.05363416;EIGEN_NC_Eigen_phred=1.64761;EIGEN_NC_Eigen_raw=-0.27013662;EIGEN_NC_FairePval=0.0;EIGEN_NC_FaireSig=0.0;EIGEN_NC_GERP_NR=0.0;EIGEN_NC_GERP_RS=0.0;EIGEN_NC_H3K27ac=62.64;EIGEN_NC_H3K4Me1=9.0;EIGEN_NC_H3K4Me3=13.04;EIGEN_NC_OCPval=0.0;EIGEN_NC_PolIIPval=0.0;EIGEN_NC_PolIISig=0.0;EIGEN_NC_TFBS_max=0.0;EIGEN_NC_TFBS_num=0.0;EIGEN_NC_TFBS_sum=0.0;EIGEN_NC_cmycPval=0.0;EIGEN_NC_cmycSig=0.0;EIGEN_NC_ctcfPval=0.0;EIGEN_NC_ctcfSig=0.0;SNVHPOL=4;SNVSB=0.0
14	1142	.	T	A	19	.	EIGEN_NC_DnasePval=0.0;EIGEN_NC_DnaseSig=0.0059;EIGEN_NC_Eigen_PC_phred=13.9238;EIGEN_NC_Eigen_PC_raw=0.7665708;EIGEN_NC_Eigen_phred=3.47555;EIGEN_NC_Eigen_raw=-0.10196207;EIGEN_NC_FairePval=5.04;EIGEN_NC_FaireSig=0.033;EIGEN_NC_GERP_NR=0.0;EIGEN_NC_GERP_RS=0.0;EIGEN_NC_H3K27ac=56.68;EIGEN_NC_H3K4Me1=7.48;EIGEN_NC_H3K4Me3=13.0;EIGEN_NC_OCPval=3.94;EIGEN_NC_PolIIPval=0.0;EIGEN_NC_PolIISig=0.004;EIGEN_NC_TFBS_max=0.0;EIGEN_NC_TFBS_num=0.0;EIGEN_NC_TFBS_sum=0.0;EIGEN_NC_cmycPval=0.0;EIGEN_NC_cmycSig=0.0254;EIGEN_NC_ctcfPval=0.0;EIGEN_NC_ctcfSig=0.0107;SNVHPOL=4;SNVSB=0.0
14	1195	.	T	A	2	.	EIGEN_NC_DnasePval=0.0;EIGEN_NC_DnaseSig=0.0059;EIGEN_NC_Eigen_PC_phred=13.9238;EIGEN_NC_Eigen_PC_raw=0.7665708;EIGEN_NC_Eigen_phred=3.47555;EIGEN_NC_Eigen_raw=-0.10196207;EIGEN_NC_FairePval=5.04;EIGEN_NC_FaireSig=0.033;EIGEN_NC_GERP_NR=0.0;EIGEN_NC_GERP_RS=0.0;EIGEN_NC_H3K27ac=56.68;EIGEN_NC_H3K4Me1=7.48;EIGEN_NC_H3K4Me3=13.0;EIGEN_NC_OCPval=3.94;EIGEN_NC_PolIIPval=0.0;EIGEN_NC_PolIISig=0.004;EIGEN_NC_TFBS_max=0.0;EIGEN_NC_TFBS_num=0.0;EIGEN_NC_TFBS_sum=0.0;EIGEN_NC_cmycPval=0.0;EIGEN_NC_cmycSig=0.0254;EIGEN_NC_ctcfPval=0.0;EIGEN_NC_ctcfSig=0.0107;SNVHPOL=4;SNVSB=0.0
14	1437	.	T	A	1	.	EIGEN_NC_DnasePval=0.0;EIGEN_NC_DnaseSig=0.0059;EIGEN_NC_Eigen_PC_phred=13.9751;EIGEN_NC_Eigen_PC_raw=0.7803033;EIGEN_NC_Eigen_phred=3.53009;EIGEN_NC_Eigen_raw=-0.09754433;EIGEN_NC_FairePval=5.04;EIGEN_NC_FaireSig=0.033;EIGEN_NC_GERP_NR=0.0;EIGEN_NC_GERP_RS=0.0;EIGEN_NC_H3K27ac=61.56;EIGEN_NC_H3K4Me1=7.64;EIGEN_NC_H3K4Me3=14.64;EIGEN_NC_OCPval=3.94;EIGEN_NC_PolIIPval=0.0;EIGEN_NC_PolIISig=0.004;EIGEN_NC_TFBS_max=0.0;EIGEN_NC_TFBS_num=0.0;EIGEN_NC_TFBS_sum=0.0;EIGEN_NC_cmycPval=0.0;EIGEN_NC_cmycSig=0.0254;EIGEN_NC_ctcfPval=0.0;EIGEN_NC_ctcfSig=0.0107;SNVHPOL=4;SNVSB=0.0
14	1659	.	G	C	8	.	EIGEN_NC_DnasePval=0.0;EIGEN_NC_DnaseSig=0.0059;EIGEN_NC_Eigen_PC_phred=14.1281;EIGEN_NC_Eigen_PC_raw=0.82222354;EIGEN_NC_Eigen_phred=3.69067;EIGEN_NC_Eigen_raw=-0.08474564;EIGEN_NC_FairePval=5.04;EIGEN_NC_FaireSig=0.033;EIGEN_NC_GERP_NR=0.0;EIGEN_NC_GERP_RS=0.0;EIGEN_NC_H3K27ac=78.24;EIGEN_NC_H3K4Me1=7.56;EIGEN_NC_H3K4Me3=18.84;EIGEN_NC_OCPval=3.94;EIGEN_NC_PolIIPval=0.0;EIGEN_NC_PolIISig=0.004;EIGEN_NC_TFBS_max=0.0;EIGEN_NC_TFBS_num=0.0;EIGEN_NC_TFBS_sum=0.0;EIGEN_NC_cmycPval=0.0;EIGEN_NC_cmycSig=0.0254;EIGEN_NC_ctcfPval=0.0;EIGEN_NC_ctcfSig=0.0107;SNVHPOL=3;SNVSB=0.0
14	1910	.	T	C	58	.	EIGEN_NC_DnasePval=0.0;EIGEN_NC_DnaseSig=0.0059;EIGEN_NC_Eigen_PC_phred=13.8695;EIGEN_NC_Eigen_PC_raw=0.75230044;EIGEN_NC_Eigen_phred=3.41565;EIGEN_NC_Eigen_raw=-0.106857374;EIGEN_NC_FairePval=5.04;EIGEN_NC_FaireSig=0.033;EIGEN_NC_GERP_NR=0.0;EIGEN_NC_GERP_RS=0.0;EIGEN_NC_H3K27ac=52.16;EIGEN_NC_H3K4Me1=5.84;EIGEN_NC_H3K4Me3=12.16;EIGEN_NC_OCPval=3.94;EIGEN_NC_PolIIPval=0.0;EIGEN_NC_PolIISig=0.004;EIGEN_NC_TFBS_max=0.0;EIGEN_NC_TFBS_num=0.0;EIGEN_NC_TFBS_sum=0.0;EIGEN_NC_cmycPval=0.0;EIGEN_NC_cmycSig=0.0254;EIGEN_NC_ctcfPval=0.0;EIGEN_NC_ctcfSig=0.0107;SNVHPOL=4;SNVSB=-10.8




```

END_DOC
*/
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;

@Program(name="vcfeigen",description="Annotator for the data of https://xioniti01.u.hpc.mssm.edu/v1.1/ : Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as made available by the ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance.")
public class VcfEigen01
	extends Launcher
	{	
	private static final Logger LOG = Logger.build(VcfEigen01.class).make();


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


	@Parameter(names={"-D","--directory"},description="Eigen directory containing the tabix files *.tab.gz")
	private String eigenDirStr = null;
	
	public VcfEigen01()
		{
		
		}
	
	@Override
	protected int doVcfToVcf(String inputName, VcfIterator r, VariantContextWriter w) {
		EigenInfoAnnotator annotator = null;
		try
			{
			
			final File eigenDirectory = new File(this.eigenDirStr);
			LOG.info("loading eigen directory "+eigenDirectory);
			annotator = new EigenInfoAnnotator(eigenDirectory);
			final VCFHeader header = r.getHeader();
			
			final  VCFHeader h2 = new VCFHeader(header);
			addMetaData(h2);
			for(final VCFInfoHeaderLine vihl: annotator.getInfoHeaderLines()) {
				if(h2.getInfoHeaderLine(vihl.getID())!=null) {
					LOG.error("VCF INFO "+vihl.getID()+" already defined in input VCF.");
					return -1;
				}
				h2.addMetaDataLine(vihl);
			}
			
			
			final  SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(header);
			w.writeHeader(h2);
			while (r.hasNext())
				{
				final  VariantContext variation = progress.watch(r.next());
				final Map<String,Object> m  = annotator.getAnnotations(variation);
				if(m==null || m.isEmpty())
					{
					w.add(variation);
					}
				else
					{
					final VariantContextBuilder vcb = new VariantContextBuilder(variation);
					for(final String key: m.keySet()) {
						vcb.attribute(key, m.get(key));
					}
					w.add(vcb.make());
					}
				}
			progress.finish();
			return RETURN_OK;
			}
		finally
			{
			CloserUtil.close(annotator);
			}
		}
	
	@Override
	public int doWork(List<String> args) {	
		if(eigenDirStr==null || eigenDirStr.trim().isEmpty()) {
			LOG.error("Eigen directory is undefined.");
			return -1;
		}
		return doVcfToVcf(args,outputFile);
		}
	
	public static void main(String[] args) throws Exception
		{
		new VcfEigen01().instanceMainWithExit(args);
		}

	}