}
groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
+ if (groups == "not found") { groups = ""; pickedGroups = false; }
else {
+ pickedGroups = true;
splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "totalgroup"; }
- if ((scale != "totalgroup") && (scale != "totalgroup") && (scale != "totalgroup") && (scale != "totalgroup")) {
+ if ((scale != "totalgroup") && (scale != "totalotu") && (scale != "averagegroup") && (scale != "averageotu")) {
m->mothurOut(scale + " is not a valid scaling option for the get.relabund command. Choices are totalgroup, totalotu, averagegroup, averageotu."); m->mothurOutEndLine(); abort = true;
}
}
m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
m->mothurOut("The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n");
m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n");
- m->mothurOut("Example get.relabund(groups=A-B-C, scale=log10).\n");
+ m->mothurOut("Example get.relabund(groups=A-B-C, scale=averagegroup).\n");
m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
m->mothurOut("The get.relabund command outputs a .relabund file.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
string outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "relabund";
ofstream out;
openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
lastLabel = lookup[0]->getLabel();
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
-
+
+ if (m->control_pressed) { globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+
//get next line to process
lookup = input->getSharedRAbundVectors();
}
}
//**********************************************************************************************************************
-int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*> thisLookUp, ofstream& out){
+int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
try {
+ if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
+
+
+ for (int i = 0; i < thisLookUp.size(); i++) {
+ out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
+
+ for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
+
+ if (m->control_pressed) { return 0; }
+
+ int abund = thisLookUp[i]->getAbundance(j);
+
+ float relabund = 0.0;
+
+ if (scale == "totalgroup") {
+ relabund = abund / (float) thisLookUp[i]->getNumSeqs();
+ }else if (scale == "totalotu") {
+ //calc the total in this otu
+ int totalOtu = 0;
+ for (int l = 0; l < thisLookUp.size(); l++) { totalOtu += thisLookUp[l]->getAbundance(j); }
+ relabund = abund / (float) totalOtu;
+ }else if (scale == "averagegroup") {
+ relabund = abund / (float) (thisLookUp[i]->getNumSeqs() / (float) thisLookUp[i]->getNumBins());
+ }else if (scale == "averageotu") {
+ //calc the total in this otu
+ int totalOtu = 0;
+ for (int l = 0; l < thisLookUp.size(); l++) { totalOtu += thisLookUp[l]->getAbundance(j); }
+ float averageOtu = totalOtu / (float) thisLookUp.size();
+
+ relabund = abund / (float) averageOtu;
+ }else{ m->mothurOut(scale + " is not a valid scaling option."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+
+ out << relabund << '\t';
+ }
+ out << endl;
+ }
-
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");
}
}
//**********************************************************************************************************************
+int GetRelAbundCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+
+ thislookup = newLookup;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
projects / mothur.git / blobdiff