/**
* Estimage the number of lines in the given file, or all files in the given directory, or all
* files referenced in a ".list" file.
*
* @param file a file or directory.
* @return
*/
private int estimateLineCount(File file) {
int nLines = 0;
if (file.isDirectory() || file.getName().endsWith(".list")) {
List<File> files = getFilesFromDirOrList(file);
for (File f : files) {
if (!f.isDirectory()) {
nLines += ParsingUtils.estimateLineCount(f.getAbsolutePath());
}
}
} else {
nLines = ParsingUtils.estimateLineCount(file.getAbsolutePath());
}
return nLines;
}
public List<Feature> getFeatures(final String chr) {
List<Feature> features = featureCache.get(chr);
if (features == null) {
final String filename = fileMap.getProperty(chr);
if (filename != null) {
BufferedReader reader = null;
String path = rootDir + "/" + filename;
try {
log.info("Loading " + path);
// Load features here
ResourceLocator loc = new ResourceLocator(path);
FeatureParser fp = AbstractFeatureParser.getInstanceFor(loc, genome);
reader = ParsingUtils.openBufferedReader(loc);
features = fp.loadFeatures(reader, genome);
featureCache.put(chr, features);
} catch (IOException ex) {
MessageUtils.showMessage("Error loading file: " + path + " (" + ex.toString() + ")");
log.info("Error loading feature file: " + filename, ex);
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {
}
}
}
}
}
return featureCache.get(chr);
}
/**
* Note: This is an exact copy of the method in ExpressionFileParser. Refactor to merge these two
* parsers, or share a common base class.
*
* @param comment
* @param dataset
*/
private void parseDirective(String comment, IGVDataset dataset) {
String tmp = comment.substring(1, comment.length());
if (tmp.startsWith("track")) {
ParsingUtils.parseTrackLine(tmp, dataset.getTrackProperties());
} else if (tmp.startsWith("columns")) {
parseColumnLine(tmp);
} else {
String[] tokens = tmp.split("=");
if (tokens.length != 2) {
return;
}
String key = tokens[0].trim().toLowerCase();
if (key.equals("name")) {
dataset.setName(tokens[1].trim());
} else if (key.equals("type")) {
try {
dataset.setTrackType(TrackType.valueOf(tokens[1].trim().toUpperCase()));
} catch (Exception exception) {
// Ignore
}
} else if (key.equals("coords")) {
startBase = Integer.parseInt(tokens[1].trim());
}
}
}
static void calculateEigenvector(String file, String chr, int binsize) throws IOException {
if (!file.endsWith("hic")) {
System.err.println("Only 'hic' files are supported");
System.exit(-1);
}
// Load the expected density function, if it exists.
Map<Integer, DensityFunction> zoomToDensityMap = null;
String densityFile = file + ".densities";
if (FileUtils.resourceExists(densityFile)) {
InputStream is = null;
try {
is = ParsingUtils.openInputStream(densityFile);
zoomToDensityMap = DensityUtil.readDensities(is);
} finally {
if (is != null) is.close();
}
} else {
System.err.println("Densities file doesn't exist");
System.exit(-1);
}
SeekableStream ss = IGVSeekableStreamFactory.getStreamFor(file);
Dataset dataset = (new DatasetReader(ss)).read();
Chromosome[] tmp = dataset.getChromosomes();
Map<String, Chromosome> chromosomeMap = new HashMap<String, Chromosome>();
for (Chromosome c : tmp) {
chromosomeMap.put(c.getName(), c);
}
if (!chromosomeMap.containsKey(chr)) {
System.err.println("Unknown chromosome: " + chr);
System.exit(-1);
}
int zoomIdx = 0;
boolean found = false;
for (; zoomIdx < HiCGlobals.zoomBinSizes.length; zoomIdx++) {
if (HiCGlobals.zoomBinSizes[zoomIdx] == binsize) {
found = true;
break;
}
}
if (!found) {
System.err.println("Unknown bin size: " + binsize);
System.exit(-1);
}
Matrix matrix = dataset.getMatrix(chromosomeMap.get(chr), chromosomeMap.get(chr));
MatrixZoomData zd = matrix.getObservedMatrix(zoomIdx);
final DensityFunction df = zoomToDensityMap.get(zd.getZoom());
double[] eigenvector = zd.computeEigenvector(df, 0);
for (double ev : eigenvector) System.out.print(ev + " ");
System.out.println();
}
private void processFrames(Element element) {
NodeList elements = element.getChildNodes();
if (elements.getLength() > 0) {
Map<String, ReferenceFrame> frames = new HashMap();
for (ReferenceFrame f : FrameManager.getFrames()) {
frames.put(f.getName(), f);
}
List<ReferenceFrame> reorderedFrames = new ArrayList();
for (int i = 0; i < elements.getLength(); i++) {
Node childNode = elements.item(i);
if (childNode.getNodeName().equalsIgnoreCase(SessionElement.FRAME.getText())) {
String frameName = getAttribute((Element) childNode, SessionAttribute.NAME.getText());
ReferenceFrame f = frames.get(frameName);
if (f != null) {
reorderedFrames.add(f);
try {
String chr = getAttribute((Element) childNode, SessionAttribute.CHR.getText());
final String startString =
getAttribute((Element) childNode, SessionAttribute.START.getText())
.replace(",", "");
final String endString =
getAttribute((Element) childNode, SessionAttribute.END.getText())
.replace(",", "");
int start = ParsingUtils.parseInt(startString);
int end = ParsingUtils.parseInt(endString);
org.broad.igv.feature.Locus locus = new Locus(chr, start, end);
f.jumpTo(locus);
} catch (NumberFormatException e) {
e.printStackTrace(); // To change body of catch statement use File | Settings |
// File Templates.
}
}
}
}
if (reorderedFrames.size() > 0) {
FrameManager.setFrames(reorderedFrames);
}
}
IGV.getInstance().resetFrames();
}
public FeatureDirSource(ResourceLocator locator, Genome genome) throws IOException {
this.genome = genome;
featureCache = new LRUCache(this, 3);
rootLocator = locator;
setRootDir(locator.getPath());
fileMap = new Properties();
InputStream propStream = ParsingUtils.openInputStreamGZ(locator);
fileMap.load(propStream);
propStream.close();
}
public void loadTDFFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
log.debug("Loading TDF file " + locator.getPath());
TDFReader reader = TDFReader.getReader(locator);
TrackType type = reader.getTrackType();
TrackProperties props = null;
String trackLine = reader.getTrackLine();
if (trackLine != null && trackLine.length() > 0) {
props = new TrackProperties();
ParsingUtils.parseTrackLine(trackLine, props);
}
// In case of conflict between the resource locator display name and the track properties name,
// use the resource locator
String name = locator.getName();
if (name != null && props != null) {
props.setName(name);
}
if (name == null) {
name = props == null ? locator.getTrackName() : props.getName();
}
int trackNumber = 0;
String path = locator.getPath();
boolean multiTrack = reader.getTrackNames().length > 1;
for (String heading : reader.getTrackNames()) {
String trackId = multiTrack ? path + "_" + heading : path;
String trackName = multiTrack ? heading : name;
final DataSource dataSource =
locator.getPath().endsWith(".counts")
? new GobyCountArchiveDataSource(locator)
: new TDFDataSource(reader, trackNumber, heading, genome);
DataSourceTrack track = new DataSourceTrack(locator, trackId, trackName, dataSource);
String displayName = (name == null || multiTrack) ? heading : name;
track.setName(displayName);
track.setTrackType(type);
if (props != null) {
track.setProperties(props);
}
newTracks.add(track);
trackNumber++;
}
}
public FastaIndexedSequence(String path) throws IOException {
this.path = path;
contentLength = ParsingUtils.getContentLength(path);
String indexPath = path + ".fai";
// The check below is not useful in the files have been copied or moved, which is always the
// case for our hosted
// genomes. It causes lots of spurious warnings
// if(ParsingUtils.getLastModified(path) > ParsingUtils.getLastModified(indexPath)){
// log.warn("Index file for " + path + " is older than the file it indexes");
// }
index = new FastaIndex(indexPath);
chromoNamesList = new ArrayList<String>(index.getSequenceNames());
}
private void loadEwigIBFFile(ResourceLocator locator, List<Track> newTracks, Genome genome) {
TDFReader reader = TDFReader.getReader(locator.getPath());
TrackProperties props = null;
String trackLine = reader.getTrackLine();
if (trackLine != null && trackLine.length() > 0) {
props = new TrackProperties();
ParsingUtils.parseTrackLine(trackLine, props);
}
EWigTrack track = new EWigTrack(locator, genome);
if (props != null) {
track.setProperties(props);
}
track.setName(locator.getTrackName());
newTracks.add(track);
}
/**
* Parse a limited number of lines in this file and return a list of features found.
*
* @param locator
* @param maxLines
* @return
*/
public List<org.broad.tribble.Feature> loadFeatures(ResourceLocator locator, int maxLines) {
BufferedReader reader = null;
try {
reader = ParsingUtils.openBufferedReader(locator);
return loadFeatures(reader, maxLines);
} catch (IOException e) {
throw new RuntimeException(e);
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {
}
}
}
}
public static boolean parsableMAGE_TAB(ResourceLocator file) throws IOException {
AsciiLineReader reader = null;
try {
reader = ParsingUtils.openAsciiReader(file);
String nextLine = null;
// skip first row
reader.readLine();
// check second row for MAGE_TAB identifiers
if ((nextLine = reader.readLine()) != null
&& (nextLine.contains("Reporter REF")
|| nextLine.contains("Composite Element REF")
|| nextLine.contains("Term Source REF")
|| nextLine.contains("CompositeElement REF")
|| nextLine.contains("TermSource REF")
|| nextLine.contains("Coordinates REF"))) {
int count = 0;
// check if this mage_tab data matrix can be parsed by this class
while ((nextLine = reader.readLine()) != null && count < 5) {
nextLine = nextLine.trim();
if (nextLine.startsWith("SNP_A") || nextLine.startsWith("CN_")) {
return true;
}
count++;
}
return false;
}
} finally {
if (reader != null) {
reader.close();
}
}
return false;
}
/**
* Load all features in this file.
*
* @param reader
* @param maxLines
* @return
*/
public List<org.broad.tribble.Feature> loadFeatures(BufferedReader reader, int maxLines) {
List<org.broad.tribble.Feature> features = new ArrayList<org.broad.tribble.Feature>();
String nextLine = null;
int nLines = 0;
try {
while ((nextLine = reader.readLine()) != null) {
nextLine = nextLine.trim();
if (nextLine.length() == 0) continue;
nLines++;
if ((maxLines > 0) && (nLines > maxLines)) {
break;
}
try {
if (nextLine.startsWith("#")) {
if (nextLine.startsWith("#type")) {
String[] tokens = Globals.equalPattern.split(nextLine);
if (tokens.length > 1) {
try {
// TODO: type is not currently used, is there any reason to keep this?
TrackType type = TrackType.valueOf(tokens[1]);
} catch (Exception e) {
log.error("Error converting track type: " + tokens[1]);
}
}
} else if (nextLine.startsWith("#track")) {
TrackProperties tp = new TrackProperties();
ParsingUtils.parseTrackLine(nextLine, tp);
setTrackProperties(tp);
if (tp.isGffTags()) {
gffTags = true;
}
} else if (nextLine.startsWith("#coords")) {
try {
String[] tokens = Globals.equalPattern.split(nextLine);
startBase = Integer.parseInt(tokens[1]);
} catch (Exception e) {
log.error("Error parsing coords line: " + nextLine, e);
}
} else if (nextLine.startsWith("#gffTags")) {
gffTags = true;
}
} else {
Feature feature = parseLine(nextLine);
if (feature != null) {
features.add(feature);
}
}
} catch (NumberFormatException e) {
// Expected condition -- for example comments. don't log as it slows down
// the parsing and is not useful information.
}
}
} catch (java.io.EOFException e) {
// This exception is due to a known bug with java zip library. Not
// in general a real error, and nothing we can do about it in any
// event.
return features;
} catch (Exception e) {
if (nextLine != null && nLines != 0) {
throw new ParserException(e.getMessage(), e, nLines, nextLine);
} else {
throw new RuntimeException(e);
}
}
// TODO -- why is this test here? This will break igvtools processing of expression files
// if (IGV.hasInstance() || Globals.isTesting()) {
FeatureDB.addFeatures(features);
// }
return features;
}
static void dumpMatrix(String file, String chr1, String chr2, int binsize, String type)
throws IOException {
if (!file.endsWith("hic")) {
System.err.println("Only 'hic' files are supported");
System.exit(-1);
}
// Load the expected density function, if it exists.
Map<Integer, DensityFunction> zoomToDensityMap = null;
if (type.equals("oe") || type.equals("pearson")) {
String densityFile = file + ".densities";
if (FileUtils.resourceExists(densityFile)) {
InputStream is = null;
try {
is = ParsingUtils.openInputStream(densityFile);
zoomToDensityMap = DensityUtil.readDensities(is);
} finally {
if (is != null) is.close();
}
} else {
System.err.println("Densities file doesn't exist, cannot calculate O/E or Pearson's");
System.exit(-1);
}
}
SeekableStream ss = IGVSeekableStreamFactory.getStreamFor(file);
Dataset dataset = (new DatasetReader(ss)).read();
Chromosome[] tmp = dataset.getChromosomes();
Map<String, Chromosome> chromosomeMap = new HashMap<String, Chromosome>();
for (Chromosome c : tmp) {
chromosomeMap.put(c.getName(), c);
}
if (!chromosomeMap.containsKey(chr1)) {
System.err.println("Unknown chromosome: " + chr1);
System.exit(-1);
} else if (!chromosomeMap.containsKey(chr2)) {
System.err.println("Unknown chromosome: " + chr2);
System.exit(-1);
}
if (type.equals("oe") || type.equals("pearson")) {
if (!chr1.equals(chr2)) {
System.err.println("Chromosome " + chr1 + " not equal to Chromosome " + chr2);
System.err.println("Currently only intrachromosomal O/E and Pearson's are supported.");
System.exit(-1);
}
}
int zoomIdx = 0;
boolean found = false;
for (; zoomIdx < HiCGlobals.zoomBinSizes.length; zoomIdx++) {
if (HiCGlobals.zoomBinSizes[zoomIdx] == binsize) {
found = true;
break;
}
}
if (!found) {
System.err.println("Unknown bin size: " + binsize);
}
Matrix matrix = dataset.getMatrix(chromosomeMap.get(chr1), chromosomeMap.get(chr2));
MatrixZoomData zd = matrix.getObservedMatrix(zoomIdx);
if (type.equals("oe") || type.equals("pearson")) {
final DensityFunction df = zoomToDensityMap.get(zd.getZoom());
if (df == null) {
System.err.println("Densities not calculated to this resolution.");
System.exit(-1);
}
zd.dumpOE(df, type.equals("oe"));
} else zd.dump();
}
private void processRootNode(Session session, Node node, HashMap additionalInformation) {
if ((node == null) || (session == null)) {
MessageUtils.showMessage("Invalid session file: root node not found");
return;
}
String nodeName = node.getNodeName();
if (!(nodeName.equalsIgnoreCase(SessionElement.GLOBAL.getText())
|| nodeName.equalsIgnoreCase(SessionElement.SESSION.getText()))) {
MessageUtils.showMessage(
"Session files must begin with a \"Global\" or \"Session\" element. Found: " + nodeName);
}
process(session, node, additionalInformation);
Element element = (Element) node;
// Load the genome, which can be an ID, or a path or URL to a .genome or indexed fasta file.
String genomeId = getAttribute(element, SessionAttribute.GENOME.getText());
if (genomeId != null && genomeId.length() > 0) {
if (genomeId.equals(GenomeManager.getInstance().getGenomeId())) {
// We don't have to reload the genome, but the gene track for the current genome should be
// restored.
Genome genome = GenomeManager.getInstance().getCurrentGenome();
IGV.getInstance().setGenomeTracks(genome.getGeneTrack());
} else {
// Selecting a genome will actually "reset" the session so we have to
// save the path and restore it.
String sessionPath = session.getPath();
if (IGV.getInstance().getGenomeIds().contains(genomeId)) {
IGV.getInstance().selectGenomeFromList(genomeId);
} else {
String genomePath = genomeId;
if (!ParsingUtils.pathExists(genomePath)) {
genomePath = FileUtils.getAbsolutePath(genomeId, session.getPath());
}
if (ParsingUtils.pathExists(genomePath)) {
try {
IGV.getInstance().loadGenome(genomePath, null);
} catch (IOException e) {
throw new RuntimeException("Error loading genome: " + genomeId);
}
} else {
MessageUtils.showMessage("Warning: Could not locate genome: " + genomeId);
}
}
session.setPath(sessionPath);
}
}
session.setLocus(getAttribute(element, SessionAttribute.LOCUS.getText()));
session.setGroupTracksBy(getAttribute(element, SessionAttribute.GROUP_TRACKS_BY.getText()));
String removeEmptyTracks = getAttribute(element, "removeEmptyTracks");
if (removeEmptyTracks != null) {
try {
Boolean b = Boolean.parseBoolean(removeEmptyTracks);
session.setRemoveEmptyPanels(b);
} catch (Exception e) {
log.error("Error parsing removeEmptyTracks string: " + removeEmptyTracks, e);
}
}
String versionString = getAttribute(element, SessionAttribute.VERSION.getText());
try {
version = Integer.parseInt(versionString);
} catch (NumberFormatException e) {
log.error("Non integer version number in session file: " + versionString);
}
session.setVersion(version);
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
// ReferenceFrame.getInstance().invalidateLocationScale();
}
/**
* 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());
}
}
public AsciiPairIterator(String path, Map<String, Integer> chromosomeOrdinals)
throws IOException {
this.reader = org.broad.igv.util.ParsingUtils.openBufferedReader(path);
this.chromosomeOrdinals = chromosomeOrdinals;
advance();
}
/**
* Scan the datafile for chromosome breaks.
*
* @param dataset
* @return
*/
public List<ChromosomeSummary> scan(IGVDataset dataset) {
int estLineCount = ParsingUtils.estimateLineCount(dataResourceLocator.getPath());
Map<String, Integer> longestFeatureMap = new HashMap();
float dataMin = 0;
float dataMax = 0;
InputStream is = null;
AsciiLineReader reader = null;
String nextLine = null;
ChromosomeSummary chrSummary = null;
List<ChromosomeSummary> chrSummaries = new ArrayList();
String[] headings = null;
WholeGenomeData wgData = null;
int nRows = 0;
int headerRows = 0;
int count = 0;
boolean logNormalized;
try {
int skipColumns = hasCalls ? 2 : 1;
// BufferedReader reader = ParsingUtils.openBufferedReader(dataResourceLocator);
is = ParsingUtils.openInputStreamGZ(dataResourceLocator);
reader = new AsciiLineReader(is);
// Infer datatype from extension. This can be overriden in the
// comment section
if (isCopyNumberFileExt(dataResourceLocator.getPath())) {
dataset.setTrackType(TrackType.COPY_NUMBER);
dataset.getTrackProperties().setWindowingFunction(WindowFunction.mean);
} else if (isLOHFileExt(dataResourceLocator.getPath())) {
dataset.setTrackType(TrackType.LOH);
dataset.getTrackProperties().setWindowingFunction(WindowFunction.mean);
} else {
dataset.getTrackProperties().setWindowingFunction(WindowFunction.mean);
}
// Parse comments and directives, if any
nextLine = reader.readLine();
while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
headerRows++;
if (nextLine.length() > 0) {
parseDirective(nextLine, dataset);
}
nextLine = reader.readLine();
}
if (chrColumn < 0) {
setColumnDefaults();
}
// Parse column headings
String[] data = nextLine.trim().split("\t");
// Set last data column
if (lastDataColumn < 0) {
lastDataColumn = data.length - 1;
}
headings = getHeadings(data, skipColumns);
dataset.setDataHeadings(headings);
// Infer if the data is logNormalized by looking for negative data values.
// Assume it is not until proven otherwise
logNormalized = false;
wgData = new WholeGenomeData(headings);
int chrRowCount = 0;
// Update
int updateCount = 5000;
long lastPosition = 0;
while ((nextLine = reader.readLine()) != null) {
if (igv != null && ++count % updateCount == 0) {
igv.setStatusBarMessage("Loaded: " + count + " / " + estLineCount + " (est)");
}
// Distance since last sample
String[] tokens = Globals.tabPattern.split(nextLine, -1);
int nTokens = tokens.length;
if (nTokens > 0) {
String thisChr = genome.getChromosomeAlias(tokens[chrColumn]);
if (chrSummary == null || !thisChr.equals(chrSummary.getName())) {
// Update whole genome and previous chromosome summary, unless this is
// the first chromosome
if (chrSummary != null) {
updateWholeGenome(chrSummary.getName(), dataset, headings, wgData);
chrSummary.setNDataPoints(nRows);
}
// Shart the next chromosome
chrSummary = new ChromosomeSummary(thisChr, lastPosition);
chrSummaries.add(chrSummary);
nRows = 0;
wgData = new WholeGenomeData(headings);
chrRowCount = 0;
}
lastPosition = reader.getPosition();
int location = -1;
try {
location = ParsingUtils.parseInt(tokens[startColumn]) - startBase;
} catch (NumberFormatException numberFormatException) {
log.error("Column " + tokens[startColumn] + " is not a number");
throw new ParserException(
"Column "
+ (startColumn + 1)
+ " must contain an integer value."
+ " Found: "
+ tokens[startColumn],
count + headerRows,
nextLine);
}
int length = 1;
if (hasEndLocations) {
try {
length = ParsingUtils.parseInt(tokens[endColumn].trim()) - location + 1;
} catch (NumberFormatException numberFormatException) {
log.error("Column " + tokens[endColumn] + " is not a number");
throw new ParserException(
"Column "
+ (endColumn + 1)
+ " must contain an integer value."
+ " Found: "
+ tokens[endColumn],
count + headerRows,
nextLine);
}
}
updateLongestFeature(longestFeatureMap, thisChr, length);
if (wgData.locations.size() > 0
&& wgData.locations.get(wgData.locations.size() - 1) > location) {
throw new ParserException(
"File is not sorted, .igv and .cn files must be sorted by start position."
+ " Use igvtools (File > Run igvtools..) to sort the file.",
count + headerRows);
}
wgData.locations.add(location);
for (int idx = 0; idx < headings.length; idx++) {
int i = firstDataColumn + idx * skipColumns;
float copyNo = i < tokens.length ? readFloat(tokens[i]) : Float.NaN;
if (!Float.isNaN(copyNo)) {
dataMin = Math.min(dataMin, copyNo);
dataMax = Math.max(dataMax, copyNo);
}
if (copyNo < 0) {
logNormalized = true;
}
String heading = headings[idx];
wgData.data.get(heading).add(copyNo);
}
nRows++;
}
chrRowCount++;
}
dataset.setLongestFeatureMap(longestFeatureMap);
} catch (ParserException pe) {
throw pe;
} catch (FileNotFoundException e) {
// DialogUtils.showError("SNP file not found: " + dataSource.getCopyNoFile());
log.error("File not found: " + dataResourceLocator);
throw new RuntimeException(e);
} catch (Exception e) {
log.error("Exception when loading: " + dataResourceLocator.getPath(), e);
if (nextLine != null && (count + headerRows != 0)) {
throw new ParserException(e.getMessage(), e, count + headerRows, nextLine);
} else {
throw new RuntimeException(e);
}
} finally {
if (is != null) {
try {
is.close();
} catch (IOException e) {
log.error("Error closing IGVDataset stream", e);
}
}
}
// Update last chromosome
if (chrSummary != null) {
updateWholeGenome(chrSummary.getName(), dataset, headings, wgData);
chrSummary.setNDataPoints(nRows);
}
dataset.setLogNormalized(logNormalized);
dataset.setDataMin(dataMin);
dataset.setDataMax(dataMax);
return chrSummaries;
}
/**
* Load data for a single chromosome.
*
* @param chrSummary
* @param dataHeaders
* @return
*/
public ChromosomeData loadChromosomeData(ChromosomeSummary chrSummary, String[] dataHeaders) {
// InputStream is = null;
try {
int skipColumns = hasCalls ? 2 : 1;
// Get an estimate of the number of snps (rows). THIS IS ONLY AN ESTIMATE
int nRowsEst = chrSummary.getNDataPts();
SeekableStream is = IGVSeekableStreamFactory.getStreamFor(dataResourceLocator.getPath());
is.seek(chrSummary.getStartPosition());
AsciiLineReader reader = new AsciiLineReader(is);
// Create containers to hold data
IntArrayList startLocations = new IntArrayList(nRowsEst);
IntArrayList endLocations = (hasEndLocations ? new IntArrayList(nRowsEst) : null);
List<String> probes = new ArrayList(nRowsEst);
Map<String, FloatArrayList> dataMap = new HashMap();
for (String h : dataHeaders) {
dataMap.put(h, new FloatArrayList(nRowsEst));
}
// Begin loop through rows
String chromosome = chrSummary.getName();
boolean chromosomeStarted = false;
String nextLine = reader.readLine();
while ((nextLine != null) && (nextLine.trim().length() > 0)) {
if (!nextLine.startsWith("#")) {
try {
String[] tokens = Globals.tabPattern.split(nextLine, -1);
String thisChromosome = genome.getChromosomeAlias(tokens[chrColumn].trim());
if (thisChromosome.equals(chromosome)) {
chromosomeStarted = true;
// chromosomeData.setMarkerId(nRows, tokens[0]);
// The probe. A new string is created to prevent holding on to the entire row through
// a substring reference
String probe = new String(tokens[probeColumn]);
probes.add(probe);
int start = ParsingUtils.parseInt(tokens[startColumn].trim()) - startBase;
if (hasEndLocations) {
endLocations.add(ParsingUtils.parseInt(tokens[endColumn].trim()));
}
startLocations.add(start);
for (int idx = 0; idx < dataHeaders.length; idx++) {
int i = firstDataColumn + idx * skipColumns;
float copyNo = i <= lastDataColumn ? readFloat(tokens[i]) : Float.NaN;
String heading = dataHeaders[idx];
dataMap.get(heading).add(copyNo);
}
} else if (chromosomeStarted) {
break;
}
} catch (NumberFormatException numberFormatException) {
// Skip line
log.info("Skipping line (NumberFormatException) " + nextLine);
}
}
nextLine = reader.readLine();
}
// Loop complete
ChromosomeData cd = new ChromosomeData(chrSummary.getName());
cd.setProbes(probes.toArray(new String[] {}));
cd.setStartLocations(startLocations.toArray());
if (hasEndLocations) {
cd.setEndLocations(endLocations.toArray());
}
for (String h : dataHeaders) {
cd.setData(h, dataMap.get(h).toArray());
}
return cd;
} catch (IOException ex) {
log.error("Error parsing cn file", ex);
throw new RuntimeException("Error parsing cn file", ex);
}
}