Added IdMapper tool

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/trunk@12 e3f1d335-44b1-4163-9530-9b341189ae98

idmapper.bat

@@ -0,0 +1 @@
+java -jar lib/bridgedb-idmapper.jar %*

idmapper.sh

@@ -0,0 +1,2 @@
+#!/bin/sh
+java -jar lib/bridgedb-idmapper.jar "$@"

idmapper/build.xml

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+<?xml version="1.0"?>
+<project name="IdMapper" default="jar" basedir=".">
+
+	<path id="project.class.path">
+		<pathelement location="build"/>
+		<pathelement location="../lib/bridgedb.jar"/>
+		<!--TODO make sure corelib build is called first -->
+	</path>
+
+	<target name="prepare">
+		<mkdir dir="build"/>
+	</target>
+
+	<target name="clean" description="Remove all generated files.">
+		<delete dir="${build.dir}"/>
+	</target>
+
+	<target name="compile" depends="prepare" description="Compile all sources">
+		<javac srcdir="src" 
+			    debug="true"	
+			    destdir="build">
+			<classpath refid="project.class.path"/>
+		</javac>
+	</target>
+
+	<target name="jar" depends="compile">
+		<jar jarfile="../bridgedb-idmapper.jar">
+			<manifest>
+				<attribute name="Main-Class" value="org.bridgedb.tools.IdMapper"/>
+				<attribute name="Class-Path" value="bridgedb.jar"/>
+			</manifest>
+			<fileset dir="build" includes="**/*.class"/>
+		</jar>
+	</target>
+
+	<target name="dist" depends="jar"/>
+</project>

idmapper/src/org/bridgedb/tools/IdMapper.java

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+// PathVisio,
+// a tool for data visualization and analysis using Biological Pathways
+// Copyright 2006-2009 BiGCaT Bioinformatics
+//
+// Licensed under the Apache License, Version 2.0 (the "License"); 
+// you may not use this file except in compliance with the License. 
+// You may obtain a copy of the License at 
+// 
+// http://www.apache.org/licenses/LICENSE-2.0 
+//  
+// Unless required by applicable law or agreed to in writing, software 
+// distributed under the License is distributed on an "AS IS" BASIS, 
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 
+// See the License for the specific language governing permissions and 
+// limitations under the License.
+//
+package org.bridgedb.tools;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.LineNumberReader;
+import java.io.PrintStream;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.bridgedb.DataDerby;
+import org.bridgedb.DataException;
+import org.bridgedb.Gdb;
+import org.bridgedb.DataSource;
+import org.bridgedb.SimpleGdbFactory;
+import org.bridgedb.Xref;
+
+public class IdMapper 
+{
+	private static class Settings
+	{
+		File fGdb = null;
+		File fInput = null;
+		File fOutput = null;
+		File fReport = null;
+		DataSource is = null;
+		DataSource os = null;
+		int inputColumn = 0; 
+		int verbose = 0; // 0, 1 or 2
+	}
+
+	public static void main(String[] args)
+	{
+		IdMapper mapper = new IdMapper();
+		mapper.run(args);
+	}
+
+	public void printUsage()
+	{
+		System.out.print (
+				"Usage:\n"+
+				"	mapper \n" +
+				"		[-v|-vv] \n" +
+				"		-g <gene database> \n " +
+				"		-i <input file> \n" +
+				"		-is <input system code> \n" +
+				"		-os <output system code> \n" +
+				"		-c <input column, 0-based> \n" +
+				"		-o <output file> \n" +
+				"		[-r <report file>] \n");
+	}
+
+	public String parseArgs(Settings settings, String[] args)
+	{
+		int pos = 0;
+		while (pos < args.length)
+		{
+			if (args[pos].equals ("-v"))
+			{
+				settings.verbose = 1;
+			} 
+			else if (args[pos].equals("-vv"))
+			{
+				settings.verbose = 2;
+			}
+			else if (args[pos].equals("-g"))
+			{
+				pos++;
+				if (pos > args.length) return "File expected after -f";
+				settings.fGdb = new File (args[pos]);
+				if (!settings.fGdb.exists()) return "File " + args[pos] + " does not exist";
+			}
+			else if (args[pos].equals("-i"))
+			{
+				pos++;
+				if (pos > args.length) return "File expected after -i";
+				settings.fInput = new File (args[pos]);
+				if (!settings.fInput.exists()) return "File " + args[pos] + " does not exist";
+			}
+			else if (args[pos].equals("-r"))
+			{
+				pos++;
+				if (pos > args.length) return "File expected after -r";
+				settings.fReport = new File (args[pos]);
+			}
+			else if (args[pos].equals("-c"))
+			{
+				pos++;
+				try
+				{
+					settings.inputColumn = Integer.parseInt (args[pos]);
+				}
+				catch (NumberFormatException ex)
+				{
+					return ex.getMessage();
+				}
+			}
+			else if (args[pos].equals("-o"))
+			{
+				pos++;
+				if (pos > args.length) return "File expected after -o";
+				settings.fOutput = new File (args[pos]);
+			}
+			else if (args[pos].equals("-is"))
+			{
+				pos++;
+				if (pos > args.length) return "System code expected after -is";
+				settings.is = DataSource.getBySystemCode(args[pos]);
+			}			
+			else if (args[pos].equals("-os"))
+			{
+				pos++;
+				if (pos > args.length) return "System code expected after -os";
+				settings.os = DataSource.getBySystemCode(args[pos]);
+			}			
+			else
+			{
+				return "Unrecognized option " + args[pos];
+			}
+			pos++;
+		}
+		if (settings.fGdb == null) return "Missing -g option";
+		if (settings.fOutput == null) return "Missing -o option";
+		if (settings.fInput == null) return "Misisng -i option";
+		if (settings.is == null) return "Missing -is option";
+		if (settings.os == null) return "Missing -os option";
+		return null;
+	}
+
+
+	public static class Mapper
+	{
+		private File fGdb = null;
+		private File fInput = null;
+		private File fOutput = null;
+		private File fReport = null;
+		private DataSource is = null;
+		private DataSource os = null;
+		private int inputColumn = 0; 
+		private int verbose = 0; // 0, 1 or 2
+
+		PrintStream report = System.out;
+		private Gdb gdb;
+
+		private List<Xref> missing = new ArrayList<Xref>();
+		private List<Xref> ambiguous = new ArrayList<Xref>();
+		int totalLines = 0;
+		int okLines = 0;
+
+		public Mapper(File fGdb, File fInput, File fOutput, File fReport, DataSource is, DataSource os, int inputColumn, int verbose)
+		{
+			this.fGdb = fGdb;
+			this.fInput = fInput;
+			this.fOutput = fOutput;
+			this.fReport = fReport;
+			this.is = is;
+			this.os = os;
+			this.inputColumn = inputColumn;
+			this.verbose = verbose;
+		}
+
+		private void connectGdb() throws DataException
+		{
+			gdb = SimpleGdbFactory.createInstance("" + fGdb, new DataDerby(), 0);
+		}
+
+		public void writeMapping() throws IOException, DataException
+		{
+			LineNumberReader reader = new LineNumberReader(new FileReader (fInput));
+			String line;
+			PrintWriter writer = new PrintWriter (new FileWriter (fOutput));
+			while ((line = reader.readLine()) != null)
+			{
+				String[] fields = line.split("\t");
+				if (fields.length > inputColumn && fields[inputColumn] != null)
+				{
+					Xref srcRef = new Xref(fields[inputColumn], is); 
+					List<Xref> destRefs = gdb.getCrossRefs(srcRef, os);
+					if (destRefs.size() == 0)
+					{
+						missing.add (srcRef);
+					}
+					else if (destRefs.size() >= 2)
+					{
+						ambiguous.add (srcRef);
+					}
+
+					if (destRefs.size() > 0)
+					{
+						okLines++;
+						// use first one
+						writer.print(destRefs.get(0).getId());
+					}
+					totalLines++;
+				}
+				writer.println("\t" + line);
+			}
+			reader.close();
+			writer.close();
+		}
+
+		public void reportMapping()
+		{
+			report.println ("Missing   : " + missing.size());
+			report.println ("Ambiguous : " + ambiguous.size());
+			report.println ("Ok        : " + okLines);
+			report.println ("           _______ +");
+			report.println ("Total     : " + totalLines);
+			report.println();
+			if (verbose >= 1)
+			{
+				// missing id's
+				report.println ("Missing id's:");
+				for (int i = 0; i < missing.size(); ++i)
+				{
+					report.print (missing.get(i));
+					if (i < missing.size()-1) report.print (", ");
+					if (i % 5 == 4) report.println();
+				}
+				report.println();
+
+				// ambiguous id's
+				report.println ("Ambiguous id's:");
+				for (int i = 0; i < ambiguous.size(); ++i)
+				{
+					report.print (ambiguous.get(i));
+					if (i < ambiguous.size()-1) report.print (", ");
+					if (i % 5 == 4) report.println();
+				}
+				report.println();
+			}
+		}
+
+		public void run()
+		{
+			try
+			{
+				if (fReport != null)
+				{
+					report = new PrintStream(new FileOutputStream(fReport));
+				}
+				connectGdb();
+				writeMapping();
+				reportMapping();
+				if (fReport != null)
+				{
+					report.close();
+				}
+			}
+			catch (IOException ex)
+			{
+				ex.printStackTrace();
+			}
+			catch (DataException ex)
+			{
+				ex.printStackTrace();
+			}
+		}
+	}
+
+	public void run(String[] args)
+	{
+		Settings settings = new Settings();
+		String error = parseArgs(settings, args);
+		if (error != null)
+		{
+			System.err.println ("Error: " + error);
+			printUsage();
+			System.exit(1);
+		}
+		Mapper mapper = new Mapper(settings.fGdb, 
+				settings.fInput, settings.fOutput, settings.fReport, 
+				settings.is, settings.os, settings.inputColumn, settings.verbose);
+		mapper.run();
+	}		
+}