//**********************************************************************************************************************
vector<string> MetaStatsCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(pthreshold);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","metastats",false,true,true); parameters.push_back(pshared);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pthreshold("threshold", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
+string MetaStatsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "metastats") { pattern = "[filename],[distance],[group],metastats"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MetaStatsCommand::MetaStatsCommand(){
try {
abort = true; calledHelp = true;
//Close all thread handles and free memory allocations.
for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->count != (pDataArray[i]->num)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->num) + " 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 j = 0; j < pDataArray[i]->outputNames.size(); j++) {
outputNames.push_back(pDataArray[i]->outputNames[j]);
string setB = namesOfGroupCombos[c][1];
//get filename
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = thisLookUp[0]->getLabel();
+ variables["[group]"] = setA + "-" + setB;
+ string outputFileName = getOutputFileName("metastats",variables);
outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
//int nameLength = outputFileName.length();
//char * output = new char[nameLength];
outputNames.pop_back();
}else {
- ofstream outTemp;
- string tempOut = outputDir + "data." + setA + "-" + setB + ".matrix";
- m->openOutputFile(tempOut, outTemp);
- for (int i = 0; i < subset.size(); i++) { outTemp << '\t' << subset[i]->getGroup(); }
- outTemp << endl;
-
-
//fill data
for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
//data[j] = new double[subset.size()];
data2[j].resize(subset.size(), 0.0);
- outTemp << "OTU" << (j+1);
+
for (int i = 0; i < subset.size(); i++) {
data2[j][i] = (subset[i]->getAbundance(j));
- outTemp << '\t' << subset[i]->getAbundance(j);
}
- outTemp << endl;
}
- outTemp.close();
+
m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine();
//metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);