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 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);
}
}
/**
* 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;
}