/**
* Load GWAS PLINK result file
*
* @param locator
* @param newTracks
* @throws IOException
*/
private void loadGWASFile(ResourceLocator locator, List<Track> newTracks, Genome genome)
throws IOException {
GWASParser gwasParser = new GWASParser(locator, genome);
GWASData gwasData = gwasParser.parse();
GWASTrack gwasTrack =
new GWASTrack(locator, locator.getPath(), locator.getFileName(), gwasData, gwasParser);
newTracks.add(gwasTrack);
}
public static Sorter getSorter(File inputFile, File outputFile) {
String shortFN = inputFile.getName().toLowerCase();
if (shortFN.endsWith(".txt")) {
shortFN = shortFN.substring(0, shortFN.length() - 4);
}
if (shortFN.endsWith(".cn")
|| shortFN.endsWith(".xcn")
|| shortFN.endsWith(".snp")
|| shortFN.endsWith(".igv")) {
return new CNSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".sam")) {
return new SAMSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".aligned")
|| shortFN.endsWith(".bed")
|| shortFN.endsWith(".bedgraph")
|| shortFN.endsWith(".bdg")) {
return new BedSorter(inputFile, outputFile);
} else if (GFFFeatureSource.isGFF(shortFN)) {
return new GFFSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".vcf")) {
return new VCFSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".psl") || shortFN.endsWith(".pslx")) {
return new BedSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".eqtl")) {
return new EQTLSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".snp")) {
return new GenericSorter(inputFile, outputFile, 1, 2);
} else if (GWASParser.isGWASFile(shortFN)) {
return new GWASSorter(inputFile, outputFile);
} else if (MUTCodec.isMutationAnnotationFile(
new ResourceLocator(inputFile.getAbsolutePath()))) {
return new MUTSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".interaction")) {
return new InteractionSorter(inputFile, outputFile);
} else if (shortFN.endsWith(".bam")) {
return new BAMSorter(inputFile, outputFile);
} else {
log.error("Unknown file type or sorting not supported for: " + inputFile.getName());
return null;
}
}
/**
* Switches on various attributes of locator (mainly locator path extension and whether the
* locator is indexed) to call the appropriate loading method.
*
* @param locator
* @param genome
* @return
*/
public List<Track> load(ResourceLocator locator, Genome genome) throws DataLoadException {
final String path = locator.getPath().trim();
log.info("Loading resource, path " + path);
try {
String typeString = locator.getTypeString();
if (typeString.endsWith(".tbi")) {
MessageUtils.showMessage(
"<html><b>Error:</b>File type '.tbi' is not recognized. If this is a 'tabix' index <br>"
+ " load the associated gzipped file, which should have an extension of '.gz'");
}
// This list will hold all new tracks created for this locator
List<Track> newTracks = new ArrayList<Track>();
String dbUrl = locator.getDBUrl();
LoadHandler handler = getTrackLoaderHandler(typeString);
if (dbUrl != null) {
this.loadFromDatabase(locator, newTracks, genome);
} else if (typeString.endsWith(".dbxml")) {
loadFromDBProfile(locator, newTracks);
} else if (typeString.endsWith(".gmt")) {
loadGMT(locator);
} else if (typeString.equals("das")) {
loadDASResource(locator, newTracks);
} else if (typeString.endsWith(".vcf.list")) {
loadVCFListFile(locator, newTracks, genome);
} else if (typeString.endsWith(".trio")) {
loadTrioData(locator);
} else if (typeString.endsWith("varlist")) {
VariantListManager.loadVariants(locator);
} else if (typeString.endsWith("samplepathmap")) {
VariantListManager.loadSamplePathMap(locator);
} else if (typeString.endsWith(".rnai.gct")) {
loadRnaiGctFile(locator, newTracks, genome);
} else if (typeString.endsWith(".gct")
|| typeString.endsWith("res")
|| typeString.endsWith("tab")) {
loadGctFile(locator, newTracks, genome);
} else if (typeString.endsWith(".gbk") || typeString.endsWith(".gb")) {
loadGbkFile(locator, newTracks, genome);
} else if (typeString.endsWith(".cn")
|| typeString.endsWith(".xcn")
|| typeString.endsWith(".snp")
|| typeString.endsWith(".igv")
|| typeString.endsWith(".loh")) {
loadIGVFile(locator, newTracks, genome);
} else if (typeString.endsWith(".cbs")
|| typeString.endsWith(".seg")
|| typeString.endsWith("glad")
|| typeString.endsWith("birdseye_canary_calls")
|| typeString.endsWith(".seg.zip")) {
loadSegFile(locator, newTracks, genome);
} else if (typeString.endsWith(".gistic")) {
loadGisticFile(locator, newTracks);
} else if (typeString.endsWith(".gs")) {
loadRNAiGeneScoreFile(locator, newTracks, RNAIGeneScoreParser.Type.GENE_SCORE, genome);
} else if (typeString.endsWith(".riger")) {
loadRNAiGeneScoreFile(locator, newTracks, RNAIGeneScoreParser.Type.POOLED, genome);
} else if (typeString.endsWith(".hp")) {
loadRNAiHPScoreFile(locator);
} else if (typeString.contains(".tabblastn") || typeString.endsWith(".orthologs")) {
loadSyntentyMapping(locator, newTracks);
} else if (typeString.endsWith(".sam")
|| typeString.endsWith(".bam")
|| typeString.endsWith(".cram")
|| typeString.endsWith(".sam.list")
|| typeString.endsWith(".bam.list")
|| typeString.endsWith(".aligned")
|| typeString.endsWith(".sai")
|| typeString.endsWith(".bai")
|| typeString.equals("alist")
|| typeString.equals(Ga4ghAPIHelper.RESOURCE_TYPE)) {
loadAlignmentsTrack(locator, newTracks, genome);
} else if (typeString.endsWith(".wig")
|| typeString.endsWith(".bedgraph")
|| typeString.endsWith(".bdg")
|| typeString.endsWith("cpg.txt")
|| typeString.endsWith(".expr")) {
loadWigFile(locator, newTracks, genome);
} else if (typeString.endsWith("fpkm_tracking")
|| typeString.endsWith("gene_exp.diff")
|| typeString.endsWith("cds_exp.diff")) {
loadCufflinksFile(locator, newTracks, genome);
} else if (typeString.contains(".dranger")) {
loadDRangerFile(locator, newTracks, genome);
} else if (typeString.endsWith(".ewig.tdf") || (typeString.endsWith(".ewig.ibf"))) {
loadEwigIBFFile(locator, newTracks, genome);
} else if (typeString.endsWith(".bw")
|| typeString.endsWith(".bb")
|| typeString.endsWith(".bigwig")
|| typeString.endsWith(".bigbed")) {
loadBWFile(locator, newTracks, genome);
} else if (typeString.endsWith(".ibf") || typeString.endsWith(".tdf")) {
loadTDFFile(locator, newTracks, genome);
} else if (typeString.endsWith(".counts")) {
loadGobyCountsArchive(locator, newTracks, genome);
} else if (WiggleParser.isWiggle(locator)) {
loadWigFile(locator, newTracks, genome);
} else if (typeString.endsWith(".maf")) {
loadMultipleAlignmentTrack(locator, newTracks, genome);
} else if (typeString.endsWith(".maf.dict")) {
loadMultipleAlignmentTrack(locator, newTracks, genome);
} else if (typeString.contains(".peak.bin")) {
loadPeakTrack(locator, newTracks, genome);
} else if (typeString.endsWith("mage-tab")
|| ExpressionFileParser.parsableMAGE_TAB(locator)) {
locator.setDescription("MAGE_TAB");
loadGctFile(locator, newTracks, genome);
} else if (typeString.endsWith(".bp")) {
loadBasePairFile(locator, newTracks, genome);
} else if (GWASParser.isGWASFile(typeString)) {
loadGWASFile(locator, newTracks, genome);
} else if (GobyAlignmentQueryReader.supportsFileType(path)) {
loadAlignmentsTrack(locator, newTracks, genome);
} else if (typeString.endsWith(".list")) {
// This should be deprecated
loadListFile(locator, newTracks, genome);
} else if (typeString.endsWith(".smap")) {
loadSMAPFile(locator, newTracks, genome);
} else if (CodecFactory.hasCodec(locator, genome) && !forceNotTribble(typeString)) {
loadTribbleFile(locator, newTracks, genome);
} else if (handler != null) {
// Custom loader specified
log.info(String.format("Loading %s with %s", path, handler));
handler.load(path, newTracks);
} else if (AttributeManager.isSampleInfoFile(locator)) {
// This might be a sample information file.
AttributeManager.getInstance().loadSampleInfo(locator);
} else {
MessageUtils.showMessage("<html>Unknown file type: " + path + "<br>Check file extension");
}
// Track line
TrackProperties tp = null;
String trackLine = locator.getTrackLine();
if (trackLine != null) {
tp = new TrackProperties();
ParsingUtils.parseTrackLine(trackLine, tp);
}
for (Track track : newTracks) {
if (locator.getFeatureInfoURL() != null) {
track.setUrl(locator.getFeatureInfoURL());
}
if (tp != null) {
track.setProperties(tp);
}
if (locator.getColor() != null) {
track.setColor(locator.getColor());
}
if (locator.getSampleId() != null) {
track.setSampleId(locator.getSampleId());
}
}
return newTracks;
} catch (Exception e) {
if (!NOLogExceptions.contains(e.getClass())) {
log.error(e.getMessage(), e);
}
throw new DataLoadException(e.getMessage());
}
}