//**********************************************************************************************************************
vector<string> GetSAbundCommand::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 plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- 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","sabund",false,false, true); parameters.push_back(plist);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false, false); parameters.push_back(pcount);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","sabund",false,false, true); parameters.push_back(prabund);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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 GetSAbundCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The get.sabund command parameters is list, rabund and label. list or rabund is required unless a valid current file exists.\n";
+ helpString += "The get.sabund command parameters is list, rabund, count and label. list or rabund is required unless a valid current file exists.\n";
+ helpString += "The count parameter allows you to provide a count file associated with your list file. If you clustered with a countfile the list file only contains the unique sequences and you will want to add the redundant counts into the sabund file, providing the count file allows you to do so.\n";
helpString += "The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n";
helpString += "The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n";
helpString += "Example get.sabund().\n";
helpString += "The default value for label is all labels in your inputfile.\n";
helpString += "The get.sabund command outputs a .sabund file containing the labels you selected.\n";
- helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
return helpString;
}
catch(exception& e) {
exit(1);
}
}
-
+//**********************************************************************************************************************
+string GetSAbundCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "sabund") { pattern = "[filename],sabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(){
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["rabund"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
- else { format = "rabund"; inputfile = rabundfile; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
-
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
}
}
+ if ((countfile != "") && (listfile == "")) { m->mothurOut("[ERROR]: You can only use the count file with a list file, aborting.\n"); abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputfile); }
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "sabund";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ filename = getOutputFileName("sabund", variables);
m->openOutputFile(filename, out);
- input = new InputData(inputfile, format);
- sabund = input->getSAbundVector();
- string lastLabel = sabund->getLabel();
-
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; }
-
-
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
+ if (countfile != "") {
+ processList(out);
+ }else {
+ InputData input(inputfile, format);
+ SAbundVector* sabund = input.getSAbundVector();
+ string lastLabel = sabund->getLabel();
+
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; return 0; }
+
+
+ while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
- delete sabund;
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; }
-
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; return 0; }
+
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- }
-
- if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ }
+
+ if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
- delete sabund;
- sabund = (input->getSAbundVector(lastLabel));
+ delete sabund;
+ sabund = (input.getSAbundVector(lastLabel));
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
- delete sabund;
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; }
-
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; return 0; }
+
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
- }
-
-
- lastLabel = sabund->getLabel();
-
- delete sabund;
- sabund = (input->getSAbundVector());
- }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (sabund != NULL) { delete sabund; }
- sabund = (input->getSAbundVector(lastLabel));
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- sabund->print(out);
- delete sabund;
-
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; return 0; }
-
+ }
+
+
+ lastLabel = sabund->getLabel();
+
+ delete sabund;
+ sabund = (input.getSAbundVector());
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (sabund != NULL) { delete sabund; }
+ sabund = (input.getSAbundVector(lastLabel));
+
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
+ sabund->print(out);
+ delete sabund;
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
+
+ }
}
-
out.close();
- delete input;
+
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(filename); return 0; }
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
m->mothurOutEndLine();
exit(1);
}
}
+//**********************************************************************************************************************
+int GetSAbundCommand::processList(ofstream& out){
+ try {
+ CountTable ct;
+ ct.readTable(countfile, false);
+
+ InputData input(inputfile, format);
+ ListVector* list = input.getListVector();
+ string lastLabel = list->getLabel();
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ if (m->control_pressed) { delete list; return 0; }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { delete list; return 0; }
+
+ RAbundVector* rabund = new RAbundVector();
+ createRabund(ct, list, rabund);
+ SAbundVector sabund = rabund->getSAbundVector();
+ sabund.print(out);
+ delete rabund;
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector(lastLabel);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { delete list; return 0; }
+
+ RAbundVector* rabund = new RAbundVector();
+ createRabund(ct, list, rabund);
+ SAbundVector sabund = rabund->getSAbundVector();
+ sabund.print(out);
+ delete rabund;
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector();
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+ list = input.getListVector(lastLabel);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { delete list; return 0; }
+
+ RAbundVector* rabund = new RAbundVector();
+ createRabund(ct, list, rabund);
+ SAbundVector sabund = rabund->getSAbundVector();
+ sabund.print(out);
+ delete rabund;
+
+ delete list;
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "processList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetSAbundCommand::createRabund(CountTable& ct, ListVector*& list, RAbundVector*& rabund){
+ try {
+
+ rabund->setLabel(list->getLabel());
+ for(int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+ vector<string> binNames;
+ string bin = list->get(i);
+ m->splitAtComma(bin, binNames);
+ int total = 0;
+ for (int j = 0; j < binNames.size(); j++) {
+ total += ct.getNumSeqs(binNames[j]);
+ }
+ rabund->push_back(total);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "createRabund");
+ exit(1);
+ }
+
+}
//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff