/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* 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,
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* THE SOFTWARE.
*/
package org.broad.igv.util;
import org.broad.igv.Globals;
import java.io.*;
import java.util.*;
/**
* Created by jrobinso on 8/28/14.
* <p/>
* 1-off utilties for manipulating 1000 genomes project files
*/
public class OneKGUtils {
static final String prefix = "http://1000genomes.s3.amazonaws.com/";
static final String prefix2 = "https://data.broadinstitute.org/igvdata/1KG/b37/";
/**
* Input files contain lines of the form
* <p/>
* data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam
*/
static void createResourceXMLs(List<String> inputFiles, String outputFile) throws IOException {
Map<String, List<String>> exomeResources = new HashMap<String, List<String>>();
Map<String, List<String>> lowCovResources = new HashMap<String, List<String>>();
Set<String> pops = new HashSet<String>();
BufferedReader br = null;
for (String inputFile : inputFiles) {
try {
br = new BufferedReader(new FileReader(inputFile));
String line;
while ((line = br.readLine()) != null) {
String[] t1 = Globals.forwardSlashPattern.split(line);
String[] t2 = t1[3].split("\\.");
String type = t2[5];
String name = t2[0] + " " + type;
String pop = t2[4];
pops.add(pop);
Map<String, List<String>> resources = type.equals("exome") ? exomeResources : lowCovResources;
List<String> entries = resources.get(pop);
if (entries == null) {
entries = new ArrayList<String>();
resources.put(pop, entries);
}
String fullPath = prefix + line;
if (!(FileUtils.resourceExists(fullPath) && FileUtils.resourceExists(fullPath + ".bai"))) {
fullPath = prefix2 + line;
}
if (!(FileUtils.resourceExists(fullPath) && FileUtils.resourceExists(fullPath + ".bai"))) {
System.out.println("Resource not found: " + line);
}
else {
entries.add("<Resource name=\"" + name + "\" path=\"" + fullPath + "\"/>");
}
}
} finally {
br.close();
}
}
PrintWriter out = null;
try {
out = new PrintWriter(outputFile);
List<String> popList = new ArrayList(pops);
Collections.sort(popList);
for (String pop : popList) {
out.println("<Category name=\"" + pop + "\">");
out.println("<Category name=\"exome\">");
List<String> entries = exomeResources.get(pop);
for (String e : entries) {
out.println(e);
}
out.println("</Category>");
out.println("<Category name=\"low coverage\">");
entries = lowCovResources.get(pop);
for (String e : entries) {
out.println(e);
}
out.println("</Category>");
out.println("</Category>");
}
} finally {
out.close();
}
}
}