//**********************************************************************************************************************
vector<string> SummaryCommand::setParameters(){
try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
- CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false,true); parameters.push_back(plist);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false); parameters.push_back(psabund);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","summary",false,false,true); parameters.push_back(pshared);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);
+ CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
+ 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); }
exit(1);
}
}
-
+//**********************************************************************************************************************
+string SummaryCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "summary") { pattern = "[filename],summary-[filename],[tag],summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SummaryCommand::SummaryCommand(){
try {
else { subsample = false; subsampleSize = -1; }
}
- if (subsample == false) { iters = 1; }
+ if (subsample == false) { iters = 0; }
else {
//if you did not set a samplesize and are not using a sharedfile
if ((subsampleSize == -1) && (format != "sharedfile")) { m->mothurOut("[ERROR]: If you want to subsample with a list, rabund or sabund file, you must provide the sample size. You can do this by setting subsample=yourSampleSize.\n"); abort=true; }
numLines = 0;
numCols = 0;
- string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
- string fileNameAve = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "ave";
- string fileNameSTD = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "std";
- outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+ string fileNameRoot = getOutputFileName("summary",variables);
+ variables["[tag]"] = "ave-std";
+ string fileNameAve = getOutputFileName("summary",variables);
+ outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
-
-
if (inputFileNames.size() > 1) {
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
groupIndex[fileNameRoot] = groups[p];
m->openOutputFile(fileNameRoot, outputFileHandle);
outputFileHandle << "label";
- ofstream outAve, outSTD;
+ ofstream outAve;
if (subsample) {
m->openOutputFile(fileNameAve, outAve);
- m->openOutputFile(fileNameSTD, outSTD);
- outputNames.push_back(fileNameAve); outputTypes["ave"].push_back(fileNameAve);
- outputNames.push_back(fileNameSTD); outputTypes["std"].push_back(fileNameSTD);
- outAve << "label"; outSTD << "label";
+ outputNames.push_back(fileNameAve); outputTypes["summary"].push_back(fileNameAve);
+ outAve << "label\tmethod";
outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
- outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint);
if (inputFileNames.size() > 1) {
groupIndex[fileNameAve] = groups[p];
- groupIndex[fileNameSTD] = groups[p];
}
}
for(int i=0;i<sumCalculators.size();i++){
if(sumCalculators[i]->getCols() == 1){
outputFileHandle << '\t' << sumCalculators[i]->getName();
- if (subsample) { outAve << '\t' << sumCalculators[i]->getName(); outSTD << '\t' << sumCalculators[i]->getName(); }
+ if (subsample) { outAve << '\t' << sumCalculators[i]->getName(); }
numCols++;
}
else{
outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
- if (subsample) { outAve << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; outSTD << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
+ if (subsample) { outAve << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
numCols += 3;
}
}
outputFileHandle << endl;
- if (subsample) { outSTD << endl; outAve << endl; }
+ if (subsample) { outAve << endl; }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
- if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- process(sabund, outputFileHandle, outAve, outSTD);
+ process(sabund, outputFileHandle, outAve);
- if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
}
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- process(sabund, outputFileHandle, outAve, outSTD);
+ process(sabund, outputFileHandle, outAve);
- if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
//restore real lastlabel to save below
sabund = input->getSAbundVector();
}
- if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
sabund = input->getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- process(sabund, outputFileHandle, outAve, outSTD);
+ process(sabund, outputFileHandle, outAve);
- if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
delete sabund;
}
outputFileHandle.close();
- if (subsample) { outAve.close(); outSTD.close(); }
+ if (subsample) { outAve.close(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
}
}
//**********************************************************************************************************************
-int SummaryCommand::process(SAbundVector*& sabund, ofstream& outputFileHandle, ofstream& outAve, ofstream& outStd) {
+int SummaryCommand::process(SAbundVector*& sabund, ofstream& outputFileHandle, ofstream& outAve) {
try {
//calculator -> data -> values
outputFileHandle << endl;
if (subsample) {
- outAve << sabund->getLabel() << '\t'; outStd << sabund->getLabel() << '\t';
+ outAve << sabund->getLabel() << '\t' << "ave\t";
//find ave and std for this label and output
//will need to modify the createGroupSummary to combine results and not mess with the .summary file.
}
}
+ outAve << endl << sabund->getLabel() << '\t' << "std\t";
for (int i = 0; i < stdDev.size(); i++) { //finds average.
for (int j = 0; j < stdDev[i].size(); j++) {
stdDev[i][j] /= (float) iters;
stdDev[i][j] = sqrt(stdDev[i][j]);
- outStd << stdDev[i][j] << '\t';
+ outAve << stdDev[i][j] << '\t';
}
}
- outAve << endl; outStd << endl;
+ outAve << endl;
}
return 0;
//open each groups summary file
vector<string> newComboNames;
- string newLabel = "";
+
map<string, map<string, vector<string> > > files;
+ map<string, string> filesTypesLabels;
+ map<string, int> filesTypesNumLines;
for (int i=0; i<outputNames.size(); i++) {
- string extension = m->getExtension(outputNames[i]);
- string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
- m->mothurRemove(combineFileName); //remove old file
-
vector<string> thisFilesLines;
ifstream temp;
m->openInputFile(outputNames[i], temp);
//read through first line - labels
- string tempLabel;
- if (i == 0) { //we want to save the labels to output below
- for (int j = 0; j < numCols+1; j++) {
- temp >> tempLabel;
-
- if (j == 1) { newLabel += "group\t" + tempLabel + '\t';
- }else{ newLabel += tempLabel + '\t'; }
- }
- }else{ for (int j = 0; j < numCols+1; j++) { temp >> tempLabel; } }
+ string labelsLine = m->getline(temp);
+ vector<string> theseLabels = m->splitWhiteSpace(labelsLine);
+
+ string newLabel = "";
+ for (int j = 0; j < theseLabels.size(); j++) {
+ if (j == 1) { newLabel += "group\t" + theseLabels[j] + '\t';
+ }else{ newLabel += theseLabels[j] + '\t'; }
+ }
m->gobble(temp);
+ int stop = numLines;
+ if (theseLabels.size() != numCols+1) { stop = numLines*2; }
//for each label
- for (int k = 0; k < numLines; k++) {
+ for (int k = 0; k < stop; k++) {
string thisLine = "";
string tempLabel;
- for (int j = 0; j < numCols+1; j++) {
+ for (int j = 0; j < theseLabels.size(); j++) {
temp >> tempLabel;
//save for later
m->gobble(temp);
}
+ string extension = m->getExtension(outputNames[i]);
+ if (theseLabels.size() != numCols+1) { extension = ".ave-std" + extension; }
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
+ m->mothurRemove(combineFileName); //remove old file
+ filesTypesLabels[extension] = newLabel;
+ filesTypesNumLines[extension] = stop;
+
map<string, map<string, vector<string> > >::iterator itFiles = files.find(extension);
if (itFiles != files.end()) { //add new files info to existing type
files[extension][outputNames[i]] = thisFilesLines;
m->openOutputFile(combineFileName, out);
//output label line to new file
- out << newLabel << endl;
+ out << filesTypesLabels[extension] << endl;
//for each label
- for (int k = 0; k < numLines; k++) {
+ for (int k = 0; k < filesTypesNumLines[extension]; k++) {
//grab summary data for each group
for (map<string, vector<string> >::iterator itType = thisType.begin(); itType != thisType.end(); itType++) {
projects / mothur.git / blobdiff