/*
* 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,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
/*
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* and open the template in the editor.
*/
package org.broad.igv.maf;
import org.broad.igv.util.ParsingUtils;
import java.io.*;
import java.util.Properties;
/**
* @author jrobinso
*/
public class MAFUtils {
public static void main(String[] args) throws IOException {
String maf = "/Users/jrobinso/projects/maf/danRer7.gasAcu1.net.maf";
createTestFile(maf, 100, 100);
}
/**
* Create a test file by keeping a sampling of blocks from the input file
*
* @param mafFile
* @param sampling
* @param maxBlocks
*/
public static void createTestFile(String mafFile, int sampling, int maxBlocks) throws IOException {
BufferedReader reader = new BufferedReader(new FileReader(mafFile));
PrintWriter pw = new PrintWriter(new BufferedWriter(new FileWriter("Test.maf")));
int a = 0;
int n = 0;
String line;
while ((line = reader.readLine()) != null && n < maxBlocks) {
if (line.startsWith("#")) {
pw.println(line);
}
String[] tokens = ParsingUtils.WHITESPACE_PATTERN.split(line);
if (tokens[0].equals("a")) {
// Peek
String tmp = reader.readLine();
tokens = ParsingUtils.WHITESPACE_PATTERN.split(tmp);
if (a % sampling == 0 && tokens[1].contains("chr")) {
pw.println();
pw.println(line);
pw.println(tmp);
while ((line = reader.readLine()) != null) {
tokens = ParsingUtils.WHITESPACE_PATTERN.split(line);
if (tokens[0].equals("a")) {
break;
} else {
pw.println(line);
}
}
}
a++;
}
}
pw.close();
reader.close();
}
}