vector<string> ShhherCommand::getValidParameters(){
try {
string Array[] = {
- "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors"
+ "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"
};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
//valid paramters for this command
string AlignArray[] = {
- "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors"
+ "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"
};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
double begClock = clock();
unsigned long int begTime = time(NULL);
-
- cout.setf(ios::fixed, ios::floatfield);
- cout.setf(ios::showpoint);
- cout << setprecision(2);
-
if(pid == 0){
processors = ncpus;
- cout << "\nGetting preliminary data..." << endl;
+ m->mothurOut("\nGetting preliminary data...\n");
getSingleLookUp();
getJointLookUp();
for(int i=0;i<numFiles;i++){
flowFileName = flowFileVector[i];
-
- cout << "\n>>>>>\tProcessing " << flowFileName << " (file " << i+1 << " of " << numFiles << ")\t<<<<<" << endl;
- cout << "Reading flowgrams..." << endl;
+
+
+
+ m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
+ m->mothurOut("Reading flowgrams...\n");
getFlowData();
- cout << "Identifying unique flowgrams..." << endl;
+
+ m->mothurOut("Identifying unique flowgrams...\n");
getUniques();
- cout << "Calculating distances between flowgrams..." << endl;
+ m->mothurOut("Calculating distances between flowgrams...\n");
char fileName[1024];
strcpy(fileName, flowFileName.c_str());
string namesFileName = createNamesFile();
- cout << "\nClustering flowgrams..." << endl;
+ m->mothurOut("\nClustering flowgrams...\n");
string listFileName = cluster(distFileName, namesFileName);
getOTUData(listFileName);
int numOTUsOnCPU = numOTUs / ncpus;
int numSeqsOnCPU = numSeqs / ncpus;
-
- cout << "\nDenoising flowgrams..." << endl;
- cout << "iter\tmaxDelta\tnLL\t\tcycletime" << endl;
+ m->mothurOut("\nDenoising flowgrams...\n");
+ m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
iter++;
- cout << iter << '\t' << maxDelta << '\t' << setprecision(2) << nLL << '\t' << time(NULL) - cycTime << '\t' << setprecision(6) << (clock() - cycClock)/(double)CLOCKS_PER_SEC << endl;
+ m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
if((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
int live = 1;
}
- cout << "\nFinalizing..." << endl;
+ m->mothurOut("\nFinalizing...\n");
fill();
setOTUs();
vector<int> otuCounts(numOTUs, 0);
remove(distFileName.c_str());
remove(namesFileName.c_str());
remove(listFileName.c_str());
-
- cout << "Total time to process " << flowFileName << ":\t" << time(NULL) - begTime << '\t' << setprecision(6) << (clock() - begClock)/(double)CLOCKS_PER_SEC << endl;
+
+ m->mothurOut("Total time to process " + toString(flowFileName) + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
}
-
}
else{
int abort = 1;
}
}
if(i % 100 == 0){
- cout << i << "\t" << (time(NULL) - begTime) << "\t" << (clock()-begClock)/CLOCKS_PER_SEC << endl;
+ m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
}
}
- cout << stopSeq << "\t" << (time(NULL) - begTime) << "\t" << (clock()-begClock)/CLOCKS_PER_SEC << endl;
+
+ m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.dist";
if(pid != 0){ fDistFileName += ".temp." + toString(pid); }
try {
if (abort == true) { return 0; }
- cout.setf(ios::fixed, ios::floatfield);
- cout.setf(ios::showpoint);
-
getSingleLookUp();
getJointLookUp();
for(int i=0;i<numFiles;i++){
flowFileName = flowFileVector[i];
- cout << "\n>>>>>\tProcessing " << flowFileName << " (file " << i+1 << " of " << numFiles << ")\t<<<<<" << endl;
- cout << "Reading flowgrams..." << endl;
+ m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
+ m->mothurOut("Reading flowgrams...\n");
getFlowData();
- cout << "Identifying unique flowgrams..." << endl;
+
+ m->mothurOut("Identifying unique flowgrams...\n");
getUniques();
- cout << "Calculating distances between flowgrams..." << endl;
+ m->mothurOut("Calculating distances between flowgrams...\n");
string distFileName = createDistFile(processors);
string namesFileName = createNamesFile();
-
- cout << "\nClustering flowgrams..." << endl;
+
+ m->mothurOut("\nClustering flowgrams...\n");
string listFileName = cluster(distFileName, namesFileName);
getOTUData(listFileName);
double begClock = clock();
unsigned long int begTime = time(NULL);
- cout << "\nDenoising flowgrams..." << endl;
- cout << "iter\tmaxDelta\tnLL\t\tcycletime" << endl;
+
+ m->mothurOut("\nDenoising flowgrams...\n");
+ m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
iter++;
- cout << iter << '\t' << maxDelta << '\t' << setprecision(2) << nLL << '\t' << time(NULL) - cycTime << '\t' << setprecision(6) << (clock() - cycClock)/(double)CLOCKS_PER_SEC << endl;
+ m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
+
}
- cout << "\nFinalizing..." << endl;
+ m->mothurOut("\nFinalizing...\n");
fill();
setOTUs();
remove(namesFileName.c_str());
remove(listFileName.c_str());
- cout << "Total time to process " << flowFileName << ":\t" << time(NULL) - begTime << '\t' << setprecision(6) << (clock() - begClock)/(double)CLOCKS_PER_SEC << endl;
+ m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
}
return 0;
}
m->openInputFile(flowFileName, flowFile);
string seqName;
+ seqNameVector.clear();
+ lengths.clear();
+ flowDataIntI.clear();
+ nameMap.clear();
+
int currentNumFlowCells;
int index = 0;
vector<short> current(numFlowCells);
- for(int j=0;j<numFlowCells;j++){ current[j] = short(((flowDataIntI[i * numFlowCells + j] + 50.0)/100.0)); }
+ for(int j=0;j<numFlowCells;j++){
+ current[j] = short(((flowDataIntI[i * numFlowCells + j] + 50.0)/100.0));
+ }
for(int j=0;j<numUniques;j++){
int offset = j * numFlowCells;
bool toEnd = 1;
- for(int k=0;k<numFlowCells;k++){
+ int shorterLength;
+ if(lengths[i] < uniqueLengths[j]) { shorterLength = lengths[i]; }
+ else { shorterLength = uniqueLengths[j]; }
+
+ for(int k=0;k<shorterLength;k++){
if(current[k] != uniqueFlowgrams[offset + k]){
toEnd = 0;
break;
mapSeqToUnique[i] = j;
uniqueCount[j]++;
index = j;
+ if(lengths[i] > uniqueLengths[j]) { uniqueLengths[j] = lengths[i]; }
break;
}
index++;
uniqueFlowDataIntI.resize(numFlowCells * numUniques);
uniqueLengths.resize(numUniques);
- flowDataPrI.assign(numSeqs * numFlowCells, 0);
+ flowDataPrI.resize(numSeqs * numFlowCells, 0);
for(int i=0;i<flowDataPrI.size();i++) { flowDataPrI[i] = getProbIntensity(flowDataIntI[i]); }
}
catch(exception& e) {
m->mothurOutEndLine();
- cout << "Total time: " << (time(NULL) - begTime) << "\t" << (clock() - begClock)/CLOCKS_PER_SEC << endl;;
+ m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
+
return fDistFileName;
}
string ShhherCommand::cluster(string distFileName, string namesFileName){
try {
- SparseMatrix* matrix;
- ListVector* list;
- RAbundVector* rabund;
globaldata->setNameFile(namesFileName);
globaldata->setColumnFile(distFileName);
clusterNameMap->readMap();
read->read(clusterNameMap);
- list = read->getListVector();
- matrix = read->getMatrix();
+ ListVector* list = read->getListVector();
+ SparseMatrix* matrix = read->getMatrix();
delete read;
delete clusterNameMap;
- rabund = new RAbundVector(list->getRAbundVector());
+ RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest");
string tag = cluster->getTag();
otuData.assign(numSeqs, 0);
cumNumSeqs.assign(numOTUs, 0);
nSeqsPerOTU.assign(numOTUs, 0);
- aaP.resize(numOTUs);
+ aaP.clear();aaP.resize(numOTUs);
+
+ seqNumber.clear();
+ aaI.clear();
+ seqIndex.clear();
string singleOTU = "";
for(int j=nSeqsPerOTU[i];j<numSeqs;j++){
aaP[i].push_back(0);
}
+
+
}
for(int i=1;i<numOTUs;i++){
seqIndex = seqNumber;
listFile.close();
+
}
catch(exception& e) {
m->errorOut(e, "ShhherCommand", "getOTUData");
try{
+
for(int i=start;i<finish;i++){
double count = 0;
for(int j=0;j<nSeqsPerOTU[i];j++){
count += singleTau[seqNumber[cumNumSeqs[i] + j]];
}
-
+
if(nSeqsPerOTU[i] > 0 && count > MIN_COUNT){
vector<double> adF(nSeqsPerOTU[i]);
vector<int> anL(nSeqsPerOTU[i]);
try{
vector<double> newTau(numOTUs,0);
vector<double> norms(numSeqs, 0);
- otuIndex.resize(0);
- seqIndex.resize(0);
- singleTau.resize(0);
+ otuIndex.clear();
+ seqIndex.clear();
+ singleTau.clear();
projects / mothur.git / blobdiff