private String generatePosExSequence(
StatAnalyser stat,
ArrayList<RegulatoryElementPWM> regElPWMs,
int sequenceLength,
int numberOfSeq)
throws DataFormatException {
String sequence = "";
final int lengthOfSection = 50;
Random rand = new Random();
int plantCtr = 0;
// Generate probabilities based on C.elegans data
/*
GeneService geneService = GeneServiceFactory.getService(GeneService.C_ELEGANS_DATA_SERVICE);
ArrayList<Feature> cElegansGenes = geneService.getGenes();
if (cElegansGenes == null){
throw new DataFormatException("SyntheticGeneService: Unable to retrieve C.elegans genes to generate positive sequences.");
}
TfbsService tfbsService = TfbsServiceFactory.getService(TfbsService.PATSER_SERVICE);
ArrayList<Feature> tfbsHits = tfbsService.getTfbsHits(cElegansGenes);
ArrayList<TfbsPWM> tfbsPWMs = tfbsService.getTfbsPWMs();
StatAnalyser stat = new StatAnalyser(tfbsHits);
*/
// OccurrencePerLocationMatrix probMtxObj = stat.getLocationalProbabilities(lengthOfSection,
// cElegansGenes.get(0).getUpstreamSequence().length(), cElegansGenes.size());
OccurrencePerLocationMatrix probMtxObj =
stat.getLocationalProbabilities(lengthOfSection, sequenceLength, numberOfSeq);
double[][] pm = probMtxObj.getProbabilityMatrix();
// int currPos = 0; //position till which the sequence has been built
for (int i = 0; i < pm.length; i++) {
ArrayList<String> regElementNames = new ArrayList<String>();
ArrayList<Double> probabilities = new ArrayList<Double>();
for (int j = 0; j < pm[i].length; j++) {
if (Double.compare(pm[i][j], 0.0) > 0) {
probabilities.add(pm[i][j]);
regElementNames.add(probMtxObj.getNamesOfTfbs().get(j));
}
}
while (!probabilities.isEmpty()) {
if (sequence.length() >= (i + 1) * lengthOfSection) {
break;
}
int randomProbabilPosition = rand.nextInt(probabilities.size());
double currProb = probabilities.get(randomProbabilPosition);
if (DataModeller.generateRandomEvent(currProb)) {
int[][] pwm = getPwmByName(regElementNames.get(randomProbabilPosition), regElPWMs);
String regElementSeq = DataModeller.getPssmSequence(pwm);
int randomPwmPosition = rand.nextInt((i + 1) * lengthOfSection - sequence.length());
String randSeq = "";
if (randomPwmPosition > 0) {
randSeq = DataModeller.getRandomSequence(randomPwmPosition, 0.25, 0.25, 0.25, 0.25);
}
sequence = sequence.concat(randSeq);
sequence = sequence.concat(regElementSeq);
plantCtr++;
}
regElementNames.remove(randomProbabilPosition);
probabilities.remove(randomProbabilPosition);
}
// fill what's left in a section with a random sequence
if (sequence.length() < (i + 1) * lengthOfSection) {
int len = (i + 1) * lengthOfSection - sequence.length();
String seq = DataModeller.getRandomSequence(len, 0.25, 0.25, 0.25, 0.25);
sequence = sequence.concat(seq);
}
}
sequence = sequence.substring(0, sequenceLength);
// TODO print
System.out.println("=== Number of PWMs planted in this sequence: " + plantCtr);
return sequence;
}