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* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
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* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
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*
* 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
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package org.broad.igv.data.rnai;
import htsjdk.tribble.readers.AsciiLineReader;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.data.expression.ProbeToLocusMap;
import org.broad.igv.exceptions.LoadResourceFromServerException;
import org.broad.igv.feature.FeatureDB;
import org.broad.igv.feature.NamedFeature;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.*;
import java.util.zip.GZIPInputStream;
/**
* Created by IntelliJ IDEA.
* User: nazaire
* Date: Feb 25, 2009
*/
public class RNAIGCTDatasetParser {
private static Logger log = Logger.getLogger(RNAIGCTDatasetParser.class);
private ResourceLocator dataFileLocator;
private int dataStartColumn = 2;
private int descriptionColumn = 1;
Genome genome;
/**
* @param gctFile
* @param genome
*/
public RNAIGCTDatasetParser(ResourceLocator gctFile, Genome genome) {
this.dataFileLocator = gctFile;
this.genome = genome;
dataStartColumn = 2;
}
public Collection<RNAIDataSource> parse() {
// Create a buffer for the string split utility. We use a custom utility as opposed
AsciiLineReader reader = null;
List dataSources = null;
String nextLine = null;
InputStream probeMappingStream = null;
try {
reader = ParsingUtils.openAsciiReader(dataFileLocator);
String headerLine = null;
// Skip header rows
nextLine = reader.readLine();
nextLine = reader.readLine();
headerLine = reader.readLine();
// Parse column headings
int skip = 1;
String[] tokens = Globals.tabPattern.split(headerLine, -1);
int nTokens = tokens.length;
String description = (nTokens > descriptionColumn)
? new String(tokens[descriptionColumn]) : null;
int nColumns = (nTokens - dataStartColumn) / skip;
String[] columnHeadings = new String[nColumns];
for (int i = 0; i < nColumns; i++) {
String heading = tokens[dataStartColumn + i * skip].replace('\"', ' ').trim();
columnHeadings[i] = heading;
}
Map<String, String[]> rnaiProbeMap = getProbeMap();
HashMap<String, HashMap<String, Float>> sampleGeneScoreMap = new HashMap();
while ((nextLine = reader.readLine()) != null) {
tokens = Globals.tabPattern.split(nextLine, -1);
nTokens = tokens.length;
String probeId = new String(tokens[0]);
float[] values = new float[nColumns];
String[] identifiers = (String[]) rnaiProbeMap.get(probeId);
String identifier = null;
if (identifiers == null || identifiers.length == 0) {
log.info("Could not find mapping for: " + probeId);
continue;
} else {
identifier = identifiers[0];
}
NamedFeature gene = FeatureDB.getFeature(identifier.toUpperCase());
if (gene == null) {
log.debug("Unknown identifier: " + identifier);
continue;
}
for (int i = 0; i < nColumns; i++) {
try {
int dataIndex = dataStartColumn + i * skip;
// If we are out of value tokens, or the cell is blank, assign NAN to the cell.
if ((dataIndex >= nTokens) || (tokens[dataIndex].length() == 0)) {
values[i] = Float.NaN;
} else {
values[i] = Float.parseFloat(tokens[dataIndex]);
}
String sample = columnHeadings[i];
RNAIHairpinValue hairpin = new RNAIHairpinValue(probeId, values[i]);
RNAIHairpinCache.getInstance().addHairpinScore(sample, gene.getName(),
hairpin);
HashMap<String, Float> geneScoreMap = sampleGeneScoreMap.get(sample);
if (geneScoreMap == null) {
geneScoreMap = new HashMap();
sampleGeneScoreMap.put(sample, geneScoreMap);
}
Float geneScore = geneScoreMap.get(gene.getName());
if (geneScore == null) {
geneScore = values[i];
geneScoreMap.put(gene.getName(), geneScore);
} else {
geneScore = new Float(Math.min(values[i], geneScore.floatValue()));
geneScoreMap.put(gene.getName(), geneScore);
}
} catch (NumberFormatException numberFormatException) {
// This is an expected condition. IGV uses NaN to
// indicate non numbers (missing data values)
values[i] = Float.NaN;
}
}
}
dataSources = computeGeneScores(sampleGeneScoreMap);
} catch (IOException ex) {
log.error("Error parsing RNAi file", ex);
throw new RuntimeException(ex);
} finally {
if (probeMappingStream != null) {
try {
probeMappingStream.close();
} catch (IOException e) {
log.error("Error closing probe mapping stream", e);
}
}
if (reader != null) {
reader.close();
}
}
return dataSources;
}
private List computeGeneScores(HashMap<String, HashMap<String, Float>> sampleGeneScoreMap) {
int confidence = 3;
List dataSources = new ArrayList();
Iterator samplesIt = sampleGeneScoreMap.keySet().iterator();
while (samplesIt.hasNext()) {
String sample = (String) samplesIt.next();
HashMap geneMap = sampleGeneScoreMap.get(sample);
RNAIDataSource ds = new RNAIDataSource(sample, "", genome);
Iterator geneScoreIt = geneMap.keySet().iterator();
while (geneScoreIt.hasNext()) {
String gene = (String) geneScoreIt.next();
Float score = (Float) geneMap.get(gene);
int numHairpins;
Collection hairpins = RNAIHairpinCache.getInstance().getHairpinScores(sample, gene);
if (hairpins == null) {
numHairpins = 0;
} else {
numHairpins = hairpins.size();
}
ds.addGeneScore(new RNAIGeneScore(sample,
FeatureDB.getFeature(gene), score.floatValue(), numHairpins));
}
dataSources.add(ds);
}
return dataSources;
}
public final static String RNAI_MAPPING_URL_KEY = "RNAI_MAPPING_URL";
private final static String DEFAULT_RNAI_MAPPING_URL = "http://www.broadinstitute.org/igv/resources/probes/rnai/RNAI_probe_mapping.txt.gz";
private static String RNAI_MAPPING_URL;
static {
if (IGV.hasInstance()) {
RNAI_MAPPING_URL = IGV.getInstance().getSession().getPersistent(RNAI_MAPPING_URL_KEY, DEFAULT_RNAI_MAPPING_URL);
} else {
RNAI_MAPPING_URL = PreferencesManager.getPreferences().getPersistent(RNAI_MAPPING_URL_KEY, DEFAULT_RNAI_MAPPING_URL);
}
}
private static Map<String, String[]> rnaiProbeMap = null;
private synchronized static Map<String, String[]> getProbeMap() throws IOException {
if (rnaiProbeMap == null) {
rnaiProbeMap = Collections.synchronizedMap(new HashMap<String, String[]>(20000));
URL url = new URL(RNAI_MAPPING_URL);
InputStream probeMappingStream = null;
try {
probeMappingStream = new GZIPInputStream(HttpUtils.getInstance().openConnectionStream(url));
BufferedReader br = new BufferedReader(new InputStreamReader(probeMappingStream));
ProbeToLocusMap.getInstance().loadMapping(br, rnaiProbeMap);
} catch (Exception e) {
throw new LoadResourceFromServerException(e.getMessage(), RNAI_MAPPING_URL, e.getClass().getSimpleName());
} finally {
if (probeMappingStream != null) {
probeMappingStream.close();
}
}
}
return rnaiProbeMap;
}
}