public String induceRulesWithTestSet(double testSetPercent) throws DataFormatException {
SystemVariables.getInstance()
.appendToExperimentNotes("\\n* Total number of PSSM matches in positive sequences: ");
// System.out.println("Total number of PSSM matches in positive sequences: ");
ArrayList<Feature> posTrainingSet =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getPositiveRegulatoryRegions(),
positiveCutOffScore,
posATcomposition,
posCGcomposition);
SystemVariables.getInstance()
.appendToExperimentNotes("\\n* Total number of PSSM matches in negative sequences: ");
// System.out.println("Total number of PSSM matches in negative sequences: ");
ArrayList<Feature> negTrainingSet =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getNegativeRegulatoryRegions(),
negativeCutOffScore,
negATcomposition,
negCGcomposition);
IlpService formatter = new IlpService(tempIlpJobDirName);
formatter.createIlpFilesWithTestSet(
regulatoryRegionService.getPositiveRegulatoryRegions(),
regulatoryRegionService.getNegativeRegulatoryRegions(),
posTrainingSet,
negTrainingSet,
testSetPercent);
String ilpTheory = formatter.runILP();
return ilpTheory;
}
public IlpService createIlpFiles() throws DataFormatException {
ArrayList<Feature> posRegElements =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getPositiveRegulatoryRegions(),
positiveCutOffScore,
posATcomposition,
posCGcomposition);
if (posRegElements == null) {
posRegElements =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getPositiveRegulatoryRegions(),
regulatoryRegionService.getNegativeRegulatoryRegions(),
positiveCutOffScore);
}
// ***** Add statistics
addMotifMatchingStatisticsToNotes("positive");
SystemVariables.getInstance().setPosSeqRelElMatchesNum(posRegElements.size());
ArrayList<Feature> negRegElements =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getNegativeRegulatoryRegions(),
negativeCutOffScore,
negATcomposition,
negCGcomposition);
if (negRegElements == null) {
negRegElements =
regulatoryElementService.getRegulatoryElements(
regulatoryRegionService.getNegativeRegulatoryRegions(), null, negativeCutOffScore);
}
// ***** Add statistics
addMotifMatchingStatisticsToNotes("negative");
SystemVariables.getInstance().setNegSeqRelElMatchesNum(negRegElements.size());
/*
System.out.println("\n Number of matches of pairs of matrices in jurkat and erythroid sequences");
String[] pwmPair = new String[]{"MA0055.1", "MA0152.1"};
System.out.println(pwmPair[0] + " and " + pwmPair[1]+" :\t" +
FeaturesTools.numSequencesContainingAll(pwmPair, posRegElements) + "\t"+
FeaturesTools.numSequencesContainingAll(pwmPair, negRegElements));
System.out.println("\nDistances between Gata and Ebox for positive sequences:");
FeaturesTools.printRegElDistances("Gata", "Ebox", posRegElements);
*/
IlpService ilpService = new IlpService(tempIlpJobDirName);
ilpService.createIlpFiles(
regulatoryRegionService.getPositiveRegulatoryRegions(),
regulatoryRegionService.getNegativeRegulatoryRegions(),
posRegElements,
negRegElements);
return ilpService;
}
/*
* Runs ILP
*/
public String induceRules() throws DataFormatException {
IlpService ilpService = createIlpFiles();
System.out.println("== Created all ILP files. Starting to induce.");
//
// ==> the star of the show
//
ilpService.runILP();
// Overwrite temporary result html footer with the one that explains how to read a theory
String htmlFooterFileName =
tempIlpJobDirName + SystemVariables.getInstance().getString("html.footer.file.name");
FileHandling.writeFile(htmlFooterFileName, FileHandling.getHTMLResultsFooter(true, true));
return "Done";
}
