VcfUcsc.java

/*
The MIT License (MIT)

Copyright (c) 2017 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.

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

import java.io.File;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

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.VCFHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;

import com.github.lindenb.jvarkit.util.vcf.VcfIterator;
import com.beust.jcommander.Parameter;
import com.github.lindenb.jvarkit.util.bio.bin.BinIterator;
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="vcfucsc",description="annotate an VCF with mysql UCSC data")
public class VcfUcsc extends Launcher
	{
	private static final Logger LOG = Logger.build(VcfUcsc.class).make();

	private static abstract class Printf
		{
		Printf next=null;
		abstract void eval(ResultSet row,StringBuilder sb) throws SQLException;
		void append(Printf n) {if( this.next==null) {this.next=n;} else this.next.append(n);}	
		}
	private static class PrintfText extends Printf
		{
		final String content;
		PrintfText(String text) {this.content=text;}
		void eval(ResultSet row,StringBuilder sb) throws SQLException
			{
			sb.append(content);
			if(next!=null) next.eval(row, sb);
			}
		}

	private static class PrintfColumnIndex extends Printf
		{
		final int column1;
		PrintfColumnIndex(int c) {this.column1=c;}
		void eval(ResultSet row,StringBuilder sb) throws SQLException
			{
			if(column1>0 || column1<=row.getMetaData().getColumnCount())
				{
				sb.append(row.getString(column1));
				}
			
			if(next!=null) next.eval(row, sb);
			}

		}

	private static class PrintfColumnLabel extends Printf
		{
		final String label;
		PrintfColumnLabel(String text) {this.label=text;}
		void eval(ResultSet row,StringBuilder sb) throws SQLException
			{
			if(!label.isEmpty())
				{
				sb.append(row.getString(label));
				}
			
			if(next!=null) next.eval(row, sb);
			}
		}

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

	@Parameter(names={"-e","--expression"},description="expression string.")
	private String expressionStr="";
	
	private Printf expression=new PrintfText("");
	
	@Parameter(names={"-D","--database"},description="database name")
	private String database="hg19";
	@Parameter(names={"-T","-t","--table"},description="table name")
	private String table=null;
	private Connection connection=null;
	private String jdbcuri="jdbc:mysql://genome-mysql.cse.ucsc.edu";
	private boolean has_bin_column=false;
	private String chromColumn=null;
	private String startColumn=null;
	private String endColumn=null;
	
	private void select(Set<String> atts,PreparedStatement pstmt) throws SQLException
		{
		ResultSet row=pstmt.executeQuery();
		while(row.next())
			{
			StringBuilder sb=new StringBuilder();
			this.expression.eval(row,sb);
			String s=sb.toString();
			if(s.isEmpty()) continue;
			atts.add(s);
			}
		row.close();
		}
	@Override
	protected int doVcfToVcf(String inputName, VcfIterator in, VariantContextWriter out) 
		{
		String TAG="UCSC_"+database.toUpperCase()+"_"+table.toUpperCase();
		PreparedStatement pstmt=null;
		ResultSet row=null;
		VCFHeader header=in.getHeader();
		
		VCFHeader h2=new VCFHeader(header.getMetaDataInInputOrder(),header.getSampleNamesInOrder());
		h2.addMetaDataLine(new VCFInfoHeaderLine(
				TAG,
				VCFHeaderLineCount.UNBOUNDED,
				VCFHeaderLineType.String,
				database+"."+table)
				);
		h2.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName()+"CmdLine",String.valueOf(getProgramCommandLine())));
		h2.addMetaDataLine(new VCFHeaderLine(getClass().getSimpleName()+"Version",String.valueOf(getVersion())));

		
		out.writeHeader(h2);
		try	{
			StringBuilder b=new StringBuilder(
					"select * from "+database+"."+table+" where ");
			b.append(chromColumn).append("=? and NOT(");
			b.append(endColumn).append("<=? or ");
			b.append(startColumn).append(">=? ) ");
			if(has_bin_column) b.append(" and bin=?");
			
			pstmt=connection.prepareStatement(b.toString());
			
			while(in.hasNext())
				{
				VariantContext ctx=in.next();
				Set<String> atts=new HashSet<String>();
				pstmt.setString(1, ctx.getContig());
				pstmt.setInt(2, ctx.getStart());
				pstmt.setInt(3, ctx.getEnd());
				if(this.has_bin_column)
					{
					BinIterator biter=new BinIterator(ctx.getStart()-1, ctx.getEnd());
					while(biter.hasNext())
						{
						pstmt.setInt(4, biter.next());
						select(atts,pstmt);
						}
					}
				else
					{
					select(atts,pstmt);
					}
				if(atts.isEmpty())
					{
					out.add(ctx);
					continue;
					}
				VariantContextBuilder vcb=new VariantContextBuilder(ctx);
				vcb.attribute(TAG,atts.toArray());
				out.add(vcb.make());
				}
			return -1;
			}
		catch(SQLException err)
			{
			throw new RuntimeException("SQLError", err);
		
			}
		finally
			{
			CloserUtil.close(row);
			CloserUtil.close(pstmt);
			}
		}

	@Override
	public int doWork(final List<String> args) {
		

		try
			{
			String s=this.expressionStr;
			while(!s.isEmpty())
				{
				int b=s.indexOf("${");
				if(b==-1)
					{
					this.expression.append(new PrintfText(s));
					break;
					}
				int e=s.indexOf("}",b);
				if(e==-1) 
					{
					LOG.error("Cannot find end of expression in "+this.expressionStr);
					return -1;
					}
				if(b>0) this.expression.append(new PrintfText(s.substring(0,b)));
				final String between = s.substring(b+2,e).trim();
				if(between.isEmpty()) 
					{
					LOG.error("bad expression in "+this.expressionStr);
					return -1;
					}
				if(between.matches("[0-9]+"))
					{
					 this.expression.append(new PrintfColumnIndex(Integer.parseInt(between)));
					}
				else
					{
					 this.expression.append(new PrintfColumnLabel(between));
					}
				s=s.substring(e+1);
				}
			}
		catch(Exception err)
			{
			LOG.error(err);
			return -1;
			}
					
			
		
		if(this.table==null)
			{
			LOG.error("Table undefined.");
			return -1;
			}
		if(this.expression==null)
			{
			LOG.error("Expression undefined.");
			return -1;
			}
		try
			{
			LOG.info("Getting jdbc-driver");
			Class.forName("com.mysql.jdbc.Driver");
			this.connection=DriverManager.getConnection(
					jdbcuri+"/"+database+"?user=genome&password=");
			Statement stmt=this.connection.createStatement();
			ResultSet row=stmt.executeQuery("describe "+database+"."+table);
			Set<String> cols=new HashSet<String>();
			while(row.next())
				{
				String colName=row.getString("Field");
				cols.add(colName);
				}
			row.close();
			stmt.close();
			this.has_bin_column=cols.contains("bin");
			
			
			for(String col:new String[]{"chrom"})
				{
				if(this.chromColumn==null && cols.contains(col))
					{
					this.chromColumn=col;
					}
				}
			if(chromColumn==null)
				{
				LOG.error("cannot find chromColumn in "+cols);
				return -1;
				}
			
			for(String col:new String[]{"txStart","cdsStart","chromStart"})
				{
				if(this.startColumn==null && cols.contains(col))
					{
					this.startColumn=col;
					}
				}
			if(startColumn==null)
				{
				LOG.error("cannot find startColumn in "+cols);
				return -1;
				}
			for(String col:new String[]{"txEnd","cdsEnd","chromEnd"})
				{
				if(this.endColumn==null && cols.contains(col))
					{
					this.endColumn=col;
					}
				}
			if(endColumn==null)
				{
				LOG.error("cannot find endColumn in "+cols);
				return -1;
				}
			return doVcfToVcf(args, outputFile);
			}
		catch(Exception err)
			{
			LOG.error(err);
			return -1;
			}
		finally
			{
			CloserUtil.close(this.connection);
			}
		}

	/**
	 * @param args
	 */
	public static void main(String[] args)
		{
		new VcfUcsc().instanceMainWithExit(args);
		}

	}