/*
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.tools;
import org.apache.log4j.Logger;
import org.broad.igv.util.HttpUtils;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.*;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
import java.util.zip.GZIPInputStream;
/**
* @author jrobinso
*/
public class TestFileGenerator {
static private Logger log = Logger.getLogger(TestFileGenerator.class);
public static void main(String[] args) {
generateTestFile("/Users/jrobinso/IGV/test_25thousand.gct", true, 25000, 100);
}
enum FileType {
CN, IGV, GCT, WIG
}
public static void generateTestFile(
String outputFile,
boolean sorted,
int nRows,
int nSamples) {
int rowsPerChr = Math.max(1, nRows / chromosome.length);
PrintWriter pw = null;
FileType type = null;
if (outputFile.endsWith(".cn")) {
type = FileType.CN;
} else if (outputFile.endsWith(".igv")) {
type = FileType.IGV;
} else if (outputFile.endsWith(".gct")) {
type = FileType.GCT;
} else if (outputFile.endsWith(".wig")) {
type = FileType.WIG;
} else {
log.error("Unsupported file type: " + outputFile);
}
try {
pw = new PrintWriter(new FileWriter(outputFile));
writeHeader(pw, nSamples, type);
Random rand = new Random();
List<String> probes = type == FileType.GCT ? getExpressionProbes() : new ArrayList();
int n = 0;
for (int i = 0; i < chromosome.length; i++) {
String chr = chromosome[i];
int len = chromSize[i];
double delta = ((double) len) / rowsPerChr;
double center = -3;
int lastStart = 0;
if (type == FileType.WIG) {
int step = (int) delta;
pw.println("fixedStep chrom=" + chr + " start=" + 1 + " step=" + step + " span=" + (step - 1));
}
for (int r = 0; r <= rowsPerChr; r++) {
int start = getStart(len, lastStart, r, delta, rand, sorted);
lastStart = start + 1;
center = 3 * ((double) start / len);
if (type == FileType.WIG) {
pw.println(center + rand.nextGaussian());
} else {
switch (type) {
case CN:
pw.print("Snp_" + r + "\t" + chr + "\t" + start);
break;
case IGV:
int end = Math.max(start + 1, (int) (start + Math.random() * 1000));
pw.print(chr + "\t" + start + "\t" + end + "\tProbe_" + r);
break;
case GCT:
String probe = probes.get(n);
pw.print(probe + "\tdesc_" + n);
}
for (int s = 0; s < nSamples; s++) {
double v = center + rand.nextGaussian();
pw.print("\t" + v);
}
pw.println();
n++;
if (n >= probes.size()) {
n = 0;
}
}
}
}
} catch (IOException e) {
log.error("Error: " + e.getMessage());
} finally{
pw.close();
}
}
public static int getChromosomeIndex(int i, boolean sorted) {
if (sorted) {
return i;
} else {
return (int) (Math.random() * 24);
}
}
public static int getStart(int len, int lastStart, int r, double delta, Random rand, boolean sorted) {
if (sorted) {
return Math.min(len, Math.max(lastStart, (int) (r * (delta - 1) - rand.nextGaussian() * delta)));
} else {
return (int) (Math.random() * len);
}
}
public static void writeHeader(PrintWriter pw, int nSamples, FileType type) {
if (type == FileType.CN) {
pw.print("Snp\tChr\tPos");
for (int s = 0; s < nSamples; s++) {
pw.print("\tSample_" + s);
}
pw.println();
} else if (type == FileType.IGV) {
pw.print("Chr\tStart\tEnd\tProbe");
for (int s = 0; s < nSamples; s++) {
pw.print("\tSample_" + s);
}
pw.println();
} else if (type == FileType.GCT) {
pw.println("ignored");
pw.println("ignored");
pw.print("Probe\tdesc");
for (int s = 0; s < nSamples; s++) {
pw.print("\tSample_" + s);
}
pw.println();
}
}
static List<String> getExpressionProbes() {
String urlString = "http://www.broadinstitute.org/igv/resources/probes/affy/affy_human_mappings.txt.gz";
AsciiLineReader bufReader = null;
List<String> probes = new ArrayList(60000);
try {
InputStream is = null;
if (HttpUtils.isRemoteURL(urlString)) {
URL url = new URL(urlString);
is = HttpUtils.getInstance().openConnectionStream(url);
} else {
is = new FileInputStream(urlString);
}
if (urlString.endsWith("gz")) {
is = new GZIPInputStream(is);
}
bufReader = new AsciiLineReader(is);
String nextLine = "";
while ((nextLine = bufReader.readLine()) != null) {
String[] tokens = nextLine.split("\t");
probes.add(tokens[0]);
}
return probes;
} catch (Exception e) {
e.printStackTrace();
return null;
} finally {
if (bufReader != null) {
bufReader.close();
}
}
}
static String[] chromosome = {
"chr1",
"chr2",
"chr3",
"chr4",
"chr5",
"chr6",
"chr7",
"chr8",
"chr9",
"chr10",
"chr11",
"chr12",
"chr13",
"chr14",
"chr15",
"chr16",
"chr17",
"chr18",
"chr19",
"chr20",
"chr21",
"chr22",
"chrX",
"chrY",
"chrM"};
static int[] chromSize = {
247249719,
242951149,
199501827,
191273063,
180857866,
170899992,
158821424,
146274826,
140273252,
135374737,
134452384,
132349534,
114142980,
106368585,
100338915,
88827254,
78774742,
76117153,
63811651,
62435964,
46944323,
49691432,
154913754,
57772954,
16571};
}