public static void main(String[] args) {
BackgroundEstimation estimation = new BolstadEMBackgroundEstimation();
// BackgroundEstimation estimation = new UniformBackgroundEstimation();
String key = args[0];
WorkflowProperties props = new WorkflowProperties();
File fplus = new File(props.getDirectory(), String.format("%s_plus.raw", key));
File fminus = new File(props.getDirectory(), String.format("%s_negative.raw", key));
// LogTransform transform = LogTransform.NONE;
LogTransform transform = LogTransform.LOG_TO_EXP;
BackgroundRemoval norm = new BackgroundRemoval(estimation, transform);
try {
System.out.println(String.format("Loading: %s", fplus.getName()));
norm.load(new WorkflowDataLoader(fplus));
System.out.println(String.format("Loading: %s", fminus.getName()));
norm.load(new WorkflowDataLoader(fminus));
WorkflowIndexing indexing = props.getIndexing(key);
System.out.println(String.format("Removing background..."));
norm.removeBackground();
Filter<ProbeLine, ProbeLine> plus =
new Filter<ProbeLine, ProbeLine>() {
public ProbeLine execute(ProbeLine p) {
return p.strand.equals("+") ? p : null;
}
};
Filter<ProbeLine, ProbeLine> minus =
new Filter<ProbeLine, ProbeLine>() {
public ProbeLine execute(ProbeLine p) {
return p.strand.equals("-") ? p : null;
}
};
System.out.println(String.format("Outputting background-removed results..."));
File plusOut = new File(props.getDirectory(), String.format("%s_plus.corrected", key));
File minusOut = new File(props.getDirectory(), String.format("%s_negative.corrected", key));
outputProbes(new FilterIterator<ProbeLine, ProbeLine>(plus, norm.iterator()), plusOut);
System.out.println(String.format("\t%s", plusOut.getAbsolutePath()));
outputProbes(new FilterIterator<ProbeLine, ProbeLine>(minus, norm.iterator()), minusOut);
System.out.println(String.format("\t%s", minusOut.getAbsolutePath()));
} catch (IOException e) {
e.printStackTrace();
}
}
public static void main(String[] args) {
WorkflowProperties props = new WorkflowProperties();
File inputFile =
args.length > 0
? new File(args[0])
: new File(props.getDirectory(), "s288c_mata_1_plus.segments");
try {
DifferentialSegments dsegs = new DifferentialSegments(inputFile);
Collection<DifferentialKey> keys = dsegs.differentialRegions(0, 1);
System.out.println(DifferentialKey.header());
for (DifferentialKey key : keys) {
System.out.println(key.toString());
}
System.out.println(String.format("# Regions: " + keys.size()));
} catch (IOException e) {
e.printStackTrace();
}
}