/*
* 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.
*/
package org.broad.igv.data.seg;
import org.broad.igv.feature.LocusScore;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import org.junit.Ignore;
import java.io.BufferedReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* @author Jim Robinson
* @date 10/15/11
*/
@Ignore
public class DBSegUtils {
public static void main(String[] args) throws IOException {
// String seg = "http://data.broadinstitute.org/igvdata/tcga/gbmsubtypes/Broad.080528.subtypes.seg.gz";
// String oFile = "gbm_subtypes.sql";
// segToDB(seg, oFile);
generateSampleInfoInserts("http://data.broadinstitute.org/igvdata/tcga/gbmsubtypes/sampleTable.txt");
}
/**
* Convert a seg file to a DB table insert (Maggie's table format)
* <p/>
* CREATE TABLE `CNV` (
* `Chromosome` varchar(255) DEFAULT NULL,
* `Start` varchar(255) DEFAULT NULL,
* `Stop` varchar(255) DEFAULT NULL,
* `Event` varchar(255) DEFAULT NULL,
* `Length` varchar(255) DEFAULT NULL,
* `% of CNV Overlap` varchar(255) DEFAULT NULL,
* `Probe Median` varchar(255) DEFAULT NULL,
* `% Heterozygous` varchar(255) DEFAULT NULL,
* `Sample` varchar(255) DEFAULT NULL
* ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
* <p/>
* -- ----------------------------
* -- Records of CNV
* -- ----------------------------
* INSERT INTO `CNV` VALUES ('chr6', '166,262,887', '170,899,992', 'Allelic Imbalance', '4637106', '52.33536872682417', '0.48076730966567993', '87.35632183908046', '44-65-05-2_T_Sty');
*
* @param segFile
* @param outputFile
*/
static void segToDB(String segFile, String outputFile) throws IOException {
ResourceLocator loc = new ResourceLocator(segFile);
SegmentedAsciiDataSet ds = new SegmentedAsciiDataSet(loc, null);
SegmentFileParser parser = new SegmentFileParser(loc);
parser.loadSegments(loc, null);
Map<String, String> sampleMap = loadSampleMappings("http://data.broadinstitute.org/igvdata/tcga/gbmsubtypes/cn.sampleMappings.txt");
PrintWriter pw = new PrintWriter(new FileWriter(outputFile));
Set<String> chrs = ds.getChromosomes();
List<String> samples = ds.getSampleNames();
for (String chr : chrs) {
for (String id : samples) {
String sample = sampleMap.get(id);
List<LocusScore> segments = ds.getSegments(id, chr);
if (segments != null && sample != null) {
for (LocusScore ls : segments) {
Segment seg = (Segment) ls;
pw.print("INSERT INTO `CNV` VALUES ('");
pw.print(chr + "', '");
pw.print(seg.getStart() + "', '");
pw.print(seg.getEnd() + "', '");
pw.print("CN', '");
int length = seg.getEnd() - seg.getStart();
pw.print(length + "', '");
pw.print("0.0', '");
pw.print(seg.getScore() + "', '");
pw.print("0', '");
pw.println(sample + "');");
}
}
}
}
pw.println("commit;");
pw.close();
}
static Map<String, String> loadSampleMappings(String file) throws IOException {
BufferedReader reader = ParsingUtils.openBufferedReader(file);
Map<String, String> map = new HashMap<String, String>();
String nextLine;
while ((nextLine = reader.readLine()) != null) {
String[] tokens = nextLine.split("\\s+");
map.put(tokens[0], tokens[1]);
}
reader.close();
return map;
}
static void generateSampleInfoInserts(String file) throws IOException {
BufferedReader reader = ParsingUtils.openBufferedReader(file);
String nextLine;
while ((nextLine = reader.readLine()) != null) {
String[] tokens = nextLine.split("\t");
if (tokens.length > 6) {
System.out.print("INSERT INTO `SAMPLE_INFO` VALUES (");
for (int i = 0; i < tokens.length; i++) {
String val = tokens[i].equals("NA") ? "" : tokens[i];
System.out.print("'" + val + "'");
if (i < tokens.length - 1) {
System.out.print(", ");
}
}
System.out.println(");");
}
}
reader.close();
}
}