/*
* 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.expression;
import htsjdk.tribble.Feature;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.feature.FeatureDB;
import org.broad.igv.feature.Locus;
import org.broad.igv.prefs.Constants;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.session.Session;
import org.broad.igv.ui.IGV;
import org.broad.igv.util.ParsingUtils;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.*;
/**
* @author jrobinso
* @date Oct 9, 2010
*/
public class GeneToLocusHelper {
private static Logger log = Logger.getLogger(GeneToLocusHelper.class);
static String LOCUS_START_DELIMITER = "|@";
static String LOCUS_END_DELIMITER = "|";
Map<String, List<Locus>> probeLocusMap;
/**
* Create an instance and loaded the supplied probe mapping file.
*
* @param probeResource - file path or URL to a bed file containing the probe mappings. CAN BE NULL.
* @throws IOException
*/
public GeneToLocusHelper(String probeResource) throws IOException {
if (probeResource != null && probeResource.trim().length() > 0) {
loadProbeMap(probeResource);
}
// If a probe file is supplied, see if there is a user default. Only do this if the custom file option
// is set and a probe mapping file has been supplied.
boolean use_probe_mf;
String userMappingFile;
if (!Globals.isHeadless()){
Session session = IGV.getInstance().getSession();
use_probe_mf = session.getPreferenceAsBoolean(Constants.USE_PROBE_MAPPING_FILE);
userMappingFile = session.getPreference(Constants.PROBE_MAPPING_FILE);
}else{
use_probe_mf = PreferencesManager.getPreferences().getAsBoolean(Constants.USE_PROBE_MAPPING_FILE);
userMappingFile = PreferencesManager.getPreferences().get(Constants.PROBE_MAPPING_FILE);
}
if (use_probe_mf) {
if (userMappingFile != null && userMappingFile.trim().length() > 0) {
loadProbeMap(userMappingFile);
}
}
}
/**
* Return a list of loci mapping to the given probe.
*
* @param probeId - the probe (or gene) ID
* @param description - optional description field. Some formats allow encoding of lcous in description fiel
* @param genomeId - the genome
* @return
*/
public List<Locus> getLoci(String probeId, String description, String genomeId) {
if (probeLocusMap != null) {
return probeLocusMap.get(probeId);
}
// Search for locus in description string. This relies on the special
// IGV convention for specifying loci (e.g |@chrX:1000-2000|
if ((description != null) && (description.length() > 3)) {
String[] locusStrings = getExplicitLocusStrings(description);
if (locusStrings != null) {
List<Locus> loci = new ArrayList(locusStrings.length);
for (String ls : locusStrings) {
ls = ls.trim();
Locus locus = getLocus(ls);
if ((locus != null) && locus.isValid()) {
loci.add(locus);
}
}
return loci;
}
}
// Search for locus from the probe name itself.
Locus locus = getLocus(probeId);
if ((locus != null) && locus.isValid()) {
return Arrays.asList(locus);
}
// See if the probes can be mapped to genes
String[] genes = ProbeToLocusMap.getInstance().getLociForProbe(probeId, genomeId);
if (genes != null) {
List<Locus> loci = new ArrayList(genes.length);
for (String g : genes) {
locus = getLocus(g);
if (locus != null) {
loci.add(locus);
}
}
return loci;
}
return null;
}
/**
* Search for a locus explicitly specified in the description field.
* A locus can be specified either directrly, as a UCSC style locus string
* (e.g. chrX:1000-2000), or indirectly as a HUGO gene symbol (e.g. egfr).
* The locus string is distinguished by the delimiters |@ and |.
*/
private String[] getExplicitLocusStrings(String description) {
// Search for locus in description string
int startIndex = description.indexOf(LOCUS_START_DELIMITER);
if (startIndex < 0) {
return null;
} else {
startIndex += 2;
}
int endIndex = description.indexOf(LOCUS_END_DELIMITER, startIndex + 1);
if (endIndex < 0) {
// Assume the locus extends to the end of the string
endIndex = description.length();
}
if (endIndex > startIndex + 3) {
String locusString = description.substring(startIndex, endIndex);
if (locusString.contains(",")) {
return locusString.split(",");
} else {
return new String[]{locusString};
}
}
return null;
}
/**
* Return a locus from the gene (e.g. EGFR) or locus (e.g. chr1:1-100) string
*/
Locus getLocus(String geneOrLocusString) {
Locus locus = Locus.fromString(geneOrLocusString);
if (locus != null && locus.isValid()) {
return locus;
} else {
// Maybe its a gene or feature
Feature gene = FeatureDB.getFeature(geneOrLocusString);
if (gene != null) {
return new Locus(gene.getChr(), gene.getStart(), gene.getEnd());
}
}
return null;
}
private void loadProbeMap(String probeResource) {
BufferedReader reader = null;
try {
probeLocusMap = new HashMap<String, List<Locus>>(50000);
int maxErrors = 10;
int errorCount = 0;
reader = ParsingUtils.openBufferedReader(probeResource);
String nextLine;
while ((nextLine = reader.readLine()) != null) {
if (nextLine.startsWith("#") || nextLine.startsWith("browser") || nextLine.startsWith("track")) {
continue;
}
String[] tokens = Globals.tabPattern.split(nextLine, -1);
if (tokens.length > 3) {
try {
String chr = tokens[0];
int start = (int) Double.parseDouble(tokens[1]);
int end = (int) Double.parseDouble(tokens[2]);
String probe = tokens[3];
Locus locus = new Locus(chr, start, end);
probeLocusMap.put(probe, Arrays.asList(locus));
} catch (NumberFormatException e) {
log.info("Skipping line: " + nextLine);
errorCount++;
if (errorCount > maxErrors) {
probeLocusMap = null;
log.info("Too many errors. Aborting.");
}
}
}
}
} catch (IOException e) {
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {
}
}
}
}
}