#include "getsabundcommand.h"
//**********************************************************************************************************************
-vector<string> GetSAbundCommand::getValidParameters(){
+vector<string> GetSAbundCommand::setParameters(){
try {
- string Array[] = {"label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "GetSAbundCommand", "getValidParameters");
+ m->errorOut(e, "GetSAbundCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-GetSAbundCommand::GetSAbundCommand(){
+string GetSAbundCommand::getHelpString(){
try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["sabund"] = tempOutNames;
+ string helpString = "";
+ 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";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
+ m->errorOut(e, "GetSAbundCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> GetSAbundCommand::getRequiredParameters(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetSAbundCommand", "getRequiredParameters");
- 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);
+ }
}
//**********************************************************************************************************************
-vector<string> GetSAbundCommand::getRequiredFiles(){
+GetSAbundCommand::GetSAbundCommand(){
try {
- string Array[] = {"list","rabund"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "GetSAbundCommand", "getRequiredFiles");
+ m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"label","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["sabund"] = tempOutNames;
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
- outputDir = "";
- outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("list");
+ //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["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("rabund");
+ //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["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; }
+ }
}
-
- //make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { m->mothurOut("You must read a list or rabund before you can use the get.sabund command."); m->mothurOutEndLine(); abort = true; }
- //check for optional parameter and set defaults
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort = true; }
+ else if (listfile == "not found") { 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; 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 (label == "not found") { label = ""; }
else { allLines = 1; }
}
- //if the user has not specified any labels use the ones from read.otu
- if(label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
-
- if (abort == false) {
- filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
- m->openOutputFile(filename, out);
+ if ((listfile == "") && (rabundfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to shared, then list, then rabund, then sabund
+ //if there is a current shared file, use it
+ listfile = m->getListFile();
+ if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ rabundfile = m->getRabundFile();
+ if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a list or rabund file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
}
+
+ 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); }
+
+
}
}
}
//**********************************************************************************************************************
-void GetSAbundCommand::help(){
- try {
- m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
- m->mothurOut("The get.sabund command parameters is label. No parameters are required.\n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
- m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
- m->mothurOut("Example get.sabund().\n");
- m->mothurOut("The default value for label is all labels in your inputfile.\n");
- m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "GetSAbundCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-GetSAbundCommand::~GetSAbundCommand(){
-}
-
-//**********************************************************************************************************************
-
int GetSAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- //using order vector so you don't have to distinguish between the list and rabund files
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- order = globaldata->gorder;
- string lastLabel = order->getLabel();
- input = globaldata->ginput;
-
- //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 order; globaldata->gorder = NULL; return 0; }
-
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ filename = getOutputFileName("sabund", variables);
+ m->openOutputFile(filename, out);
- while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if(allLines == 1 || labels.count(order->getLabel()) == 1){
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- sabund = new SAbundVector();
- *sabund = (order->getSAbundVector());
+ 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 order; globaldata->gorder = NULL; return 0; }
-
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
- }
-
- if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = order->getLabel();
+ 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)) {
+ string saveLabel = sabund->getLabel();
- delete order;
- order = (input->getOrderVector(lastLabel));
+ delete sabund;
+ sabund = (input.getSAbundVector(lastLabel));
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- sabund = new SAbundVector();
- *sabund = (order->getSAbundVector());
+ m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
- delete sabund;
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
-
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
+ 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
- order->setLabel(saveLabel);
- }
-
-
- lastLabel = order->getLabel();
-
- delete order;
- order = (input->getOrderVector());
- }
-
- //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();
- }
+ 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(); m->mothurRemove(filename); return 0; }
+
+ }
}
-
- //run last label if you need to
- if (needToRun == true) {
- if (order != NULL) { delete order; }
- order = (input->getOrderVector(lastLabel));
-
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- sabund = new SAbundVector();
- *sabund = (order->getSAbundVector());
- sabund->print(out);
- delete sabund;
-
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
-
- delete order;
- }
- globaldata->gorder = NULL;
-
out.close();
+
+ 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();
+ //set sabund file as new current sabundfile
+ string current = "";
+ itTypes = outputTypes.find("sabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
+ }
+
return 0;
}
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);
+ }
+
+}
//**********************************************************************************************************************
+
+
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