int main(int argc, char* argv[]) {
std::string searchFile(argv[2]);
uint topN(std::stoi(argv[3]));
std::ifstream corpus(argv[1]);
std::istream_iterator<std::string> corpus_it(corpus), eof;
std::vector<std::string> fileList(corpus_it, eof);
strIntMap corpusMap, documentMap;
std::cout << "Loading corpus using files listed in " << argv[1]
<< std::endl;
loadCorpusAndSearchFiles(corpusMap, documentMap, searchFile, fileList);
std::cout << "Loaded corpus of " << corpusMap.size() << " words from "
<< fileList.size() << " file(s)" << std::endl
<< "------[ Starting analysis ]------" << std::endl << "Top "
<< topN << " significant words..." << std::endl;
std::set<tfidfPair> result;
getTopN(topN, fileList.size(), result, documentMap, corpusMap);
printTopN(result);
std::cout << "Lines with 1 or more significant words:" << std::endl;
countSigWords(searchFile, result);
return 0;
}
void reads::detectBS()
{
param.fragLengthMean += param.smoothArm; // add the soomth arm to the average length
//param.fragLengthVar = param.fragLengthMean * param.fragLengthMean / 8.0;
param.fragLengthVar = param.fragLengthMean * param.fragLengthMean / 10.0;
//param.fragLengthVar = param.fragLengthMean * 20.0;
param.lmLength = (int) (0.8 * param.fragLengthMean);
param.lmArm = param.lmLength / 2;
vector<int> f_maxPos, r_maxPos;
vector<double> f_max, r_max, tmp, tmp2;
//double R2_theshold = param.R2_cutoff;
int i, j;
int totalRC = readsClusterVec.size();
//int arm = param.smoothArm + param.lmArm;
int arm;
if (param.smoothArm > 0)
arm = param.smoothArm + param.lmArm + 5; //param.motifWidth / 4; // add the half motif width for shift the binding site a litter farther from the signal
else
arm = 3 * param.smoothBandwidth + param.lmArm + 5; //param.motifWidth / 4;
vector<readsCluster> sub_rcv;
char strand;
double pval;
double foldChange;
double qval1, qval2;
int chrIdx;
int pos = 0;
double R2 = 0;
double slope = 0;
if (totalRC == 0)
return;
// for linear model
lm *lm_signal;
lm_signal = new lm();
lm_signal->generateX();
sort(readsClusterVec.begin(), readsClusterVec.end(), mem_fun_ref(&readsCluster::sortByPos));
for (i=0; i<totalRC; i++)
{
strand = readsClusterVec[i].r_strand;
chrIdx = readsClusterVec[i].r_chrIdx;
pval = readsClusterVec[i].pval;
foldChange = readsClusterVec[i].foldChange;
qval1 = readsClusterVec[i].qval1;
qval2 = readsClusterVec[i].qval2;
if (strand == 'f' || strand == '+')
{
if (lm_signal->slipSolve(readsClusterVec[i].r_vec, 'f'))
{
logVec(lm_signal->slopeVec, tmp);
multiVec(tmp, lm_signal->R2Vec, tmp2);
//printf("fwd R2 slope log_slope R2*log_slope vecs:\n");
//printVec(lm_signal->R2Vec);
//printVec(lm_signal->slopeVec);
//printVec(tmp);
//printVec(tmp2);
getTopN(tmp2, lm_signal->slopeVec, f_max, f_maxPos, 2, param.motifWidth);
//getTopN(lm_signal->R2Vec, lm_signal->slopeVec, f_max, f_maxPos, 2, param.motifWidth);
for (j=0; j<(int)f_maxPos.size(); j++)
{
pos = readsClusterVec[i].r_end + arm - f_maxPos[j];
R2 = lm_signal->R2Vec[f_maxPos[j]];
slope = lm_signal->slopeVec[f_maxPos[j]];
bingdingSite newBS(chrIdx, pos, R2, slope, strand, pval, foldChange, qval1, qval2);
BSVec.push_back(newBS);
if (slope > maxSlope)
maxSlope = slope;
if (R2 > maxR2)
maxR2 = R2;
if (foldChange > maxFC)
maxFC = foldChange;
/*if (lm_signal->R2Vec[f_maxPos[j]] > R2_theshold)
{
bingdingSite newBS(readsClusterVec[i].r_chrIdx, readsClusterVec[i].r_end + arm - f_maxPos[j], lm_signal->R2Vec[f_maxPos[j]], lm_signal->slopeVec[f_maxPos[j]], '+');
//printf("%d\t%d\t%d\t%d\t%f\t%f\t+\n",readsClusterVec[i].r_end, arm, f_maxPos[j], readsClusterVec[i].r_end + arm - f_maxPos[j], lm_signal->R2Vec[f_maxPos[j]], lm_signal->slopeVec[f_maxPos[j]]);
BSVec.push_back(newBS);
if (lm_signal->slopeVec[f_maxPos[j]] > maxSlope)
maxSlope = lm_signal->slopeVec[f_maxPos[j]];
}*/
}
}
}
if (strand == 'r' || strand == '-')
{
if (lm_signal->slipSolve(readsClusterVec[i].r_vec, 'r'))
{
logVec(lm_signal->slopeVec, tmp);
multiVec(tmp, lm_signal->R2Vec, tmp2);
//printf("rvs R2 slope log_slope R2*log_slope vecs:\n");
//printVec(lm_signal->R2Vec);
//printVec(lm_signal->slopeVec);
//printVec(tmp);
//printVec(tmp2);
getTopN(tmp2, lm_signal->slopeVec, r_max, r_maxPos, 2, param.motifWidth);
//getTopN(lm_signal->R2Vec, lm_signal->slopeVec, r_max, r_maxPos, 2, param.motifWidth);
for (j=0; j<(int)r_maxPos.size(); j++)
{
pos = readsClusterVec[i].r_start - arm + r_maxPos[j];
R2 = lm_signal->R2Vec[r_maxPos[j]];
slope = lm_signal->slopeVec[r_maxPos[j]];
bingdingSite newBS(chrIdx, pos, R2, slope, strand, pval, foldChange, qval1, qval2);
BSVec.push_back(newBS);
if (slope > maxSlope)
maxSlope = slope;
if (R2 > maxR2)
maxR2 = R2;
if (foldChange > maxFC)
maxFC = foldChange;
/*if (lm_signal->R2Vec[r_maxPos[j]] > R2_theshold)
{
bingdingSite newBS(readsClusterVec[i].r_chrIdx, readsClusterVec[i].r_start - arm + r_maxPos[j], lm_signal->R2Vec[r_maxPos[j]], lm_signal->slopeVec[r_maxPos[j]], '-');
//printf("%d\t%d\t%d\t%d\t%f\t%f\t-\n",readsClusterVec[i].r_start, arm, r_maxPos[j], readsClusterVec[i].r_start - arm + r_maxPos[j], lm_signal->R2Vec[r_maxPos[j]], lm_signal->slopeVec[r_maxPos[j]]);
BSVec.push_back(newBS);
if (lm_signal->slopeVec[r_maxPos[j]] > maxSlope)
maxSlope = lm_signal->slopeVec[r_maxPos[j]];
}*/
}
}
}
//chrIdx(chrIdx), pos(pos), R2(R2), slope(slope), strand(strand), pval(pval), foldChange(foldChange),qval(qval)
/*if (param.VERBOSE && i % 100 == 0)
printf(" %.2f%% done...\r", 100.0 * (double) i / (double) totalRC);*/
}
}
