CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
- CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
- CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square-column", "lt", "", "", "","",false,false); parameters.push_back(poutput);
CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
- helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
+ helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, column and square. The default is lt.\n";
helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
}
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
- if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
+ if ((output != "lt") && (output != "square") && (output != "column")) { m->mothurOut(output + " is not a valid output form. Options are lt, column and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
mode = validParameter.validFile(parameters, "mode", false); if(mode == "not found"){ mode = "average"; }
if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
matrixCalculators.push_back(new MemEuclidean());
}else if (Estimators[i] == "mempearson") {
matrixCalculators.push_back(new MemPearson());
+ }else if (Estimators[i] == "jsd") {
+ matrixCalculators.push_back(new JSD());
+ }else if (Estimators[i] == "rjsd") {
+ matrixCalculators.push_back(new RJSD());
}
}
}
string current = "";
itTypes = outputTypes.find("phylip");
if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; if (!subsample) { m->setPhylipFile(current); } }
}
m->mothurOutEndLine();
try {
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- //output num seqs
- out << simMatrix.size() << endl;
-
+
if (output == "lt") {
+ out << simMatrix.size() << endl;
for (int b = 0; b < simMatrix.size(); b++) {
out << lookup[b]->getGroup() << '\t';
for (int n = 0; n < b; n++) {
}
out << endl;
}
+ }else if (output == "column") {
+ for (int b = 0; b < simMatrix.size(); b++) {
+ for (int n = 0; n < b; n++) {
+ out << lookup[b]->getGroup() << '\t' << lookup[n]->getGroup() << '\t' << simMatrix[b][n] << endl;
+ }
+ }
}else{
+ out << simMatrix.size() << endl;
for (int b = 0; b < simMatrix.size(); b++) {
out << lookup[b]->getGroup() << '\t';
for (int n = 0; n < simMatrix[b].size(); n++) {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
- int pid = fork();
+ pid_t pid = fork();
if (pid > 0) {
processIDS.push_back(pid);
driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);
- string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
+ string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + m->mothurGetpid(process) + ".dist";
ofstream outtemp;
m->openOutputFile(tempdistFileName, outtemp);
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
+ }
for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; }
for (int k = 0; k < calcDists.size(); k++) {
}
if (subsample && (thisIter != 0)) {
- if((thisIter) % 100 == 0){ m->mothurOut(toString(thisIter)); m->mothurOutEndLine(); }
+ if((thisIter) % 100 == 0){ m->mothurOutJustToScreen(toString(thisIter)+"\n"); }
calcDistsTotals.push_back(calcDists);
for (int i = 0; i < calcDists.size(); i++) {
for (int j = 0; j < calcDists[i].size(); j++) {
variables["[calc]"] = matrixCalculators[i]->getName();
string distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+ //set current phylip file to average distance matrix
+ m->setPhylipFile(distFileName);
ofstream outAve;
m->openOutputFile(distFileName, outAve);
outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
if (m->control_pressed) { return 1; }
-
+
seqDist temp(l, k, tempdata[0]);
calcDists[i].push_back(temp);
}
projects / mothur.git / blobdiff