#include "getrabundcommand.h"
//**********************************************************************************************************************
-vector<string> GetRAbundCommand::getValidParameters(){
+vector<string> GetRAbundCommand::setParameters(){
try {
- string Array[] = {"label","sorted","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(plist);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none","",false,false, false); parameters.push_back(pcount);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(psabund);
+ CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(psorted);
+ 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, "GetRAbundCommand", "getValidParameters");
+ m->errorOut(e, "GetRAbundCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-GetRAbundCommand::GetRAbundCommand(){
+string GetRAbundCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["rabund"] = tempOutNames;
+ string helpString = "";
+ helpString += "The get.rabund command parameters are list, sabund, count, label and sorted. list or sabund parameters are required, unless you have valid current files.\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 rabund 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 .rabund file, and are separated by dashes.\n";
+ helpString += "The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n";
+ helpString += "The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n";
+ helpString += "Example get.rabund(sorted=F).\n";
+ helpString += "The default value for label is all labels in your inputfile.\n";
+ helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
+ m->errorOut(e, "GetRAbundCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> GetRAbundCommand::getRequiredParameters(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetRAbundCommand", "getRequiredParameters");
- exit(1);
- }
+string GetRAbundCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "rabund") { pattern = "[filename],rabund"; }
+ 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> GetRAbundCommand::getRequiredFiles(){
+GetRAbundCommand::GetRAbundCommand(){
try {
- string Array[] = {"list"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "GetRAbundCommand", "getRequiredFiles");
+ m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
GetRAbundCommand::GetRAbundCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
//allow user to run help
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","sorted","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; }
}
- //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
- }
-
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["rabund"] = tempOutNames;
- //make sure the user has already run the read.otu command
- if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; }
+ //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("sabund");
+ //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["sabund"] = 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; }
+ }
+ }
+
+
+ //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); }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { sabundfile = ""; abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
+
+ 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...
-
string temp;
temp = validParameter.validFile(parameters, "sorted", false); if (temp == "not found") { temp = "T"; }
sorted = m->isTrue(temp);
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)) + "rabund";
- m->openOutputFile(filename, out);
+ if ((listfile == "") && (sabundfile == "")) {
+ //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 {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a list or sabund 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); }
+
}
+
}
catch(exception& e) {
}
//**********************************************************************************************************************
-void GetRAbundCommand::help(){
- try {
- m->mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
- m->mothurOut("The get.rabund command parameters are label and sorted. No parameters are required.\n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
- m->mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n");
- m->mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n");
- m->mothurOut("Example get.rabund(sorted=F).\n");
- m->mothurOut("The default value for label is all labels in your inputfile.\n");
- m->mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "GetRAbundCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-GetRAbundCommand::~GetRAbundCommand(){}
-
-//**********************************************************************************************************************
-
int GetRAbundCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- //read first line
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- list = globaldata->gListVector;
- string lastLabel = list->getLabel();
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ filename = getOutputFileName("rabund", variables);
+ m->openOutputFile(filename, out);
- //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 list; globaldata->gListVector = NULL; return 0; }
-
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if(allLines == 1 || labels.count(list->getLabel()) == 1){
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- rabund = new RAbundVector();
- *rabund = (list->getRAbundVector());
+ if (countfile != "") {
+ processList(out);
+ }else {
+ InputData input(inputfile, format);
+ RAbundVector* rabund = input.getRAbundVector();
+ string lastLabel = rabund->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 rabund; return 0; }
+
+ while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; }
-
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
+
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = rabund->getLabel();
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);
+ rabund = input.getRAbundVector(lastLabel);
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- rabund = new RAbundVector();
- *rabund = (list->getRAbundVector());
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
-
- delete rabund;
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
+
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->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();
- }
+ rabund->setLabel(saveLabel);
+ }
+
+ lastLabel = rabund->getLabel();
+
+ delete rabund;
+ rabund = input.getRAbundVector();
+ }
+
+ //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 (rabund != NULL) { delete rabund; }
+ rabund = input.getRAbundVector(lastLabel);
+
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
+
+ if(sorted) { rabund->print(out); }
+ else { rabund->nonSortedPrint(out); }
+
+ delete rabund;
+ }
}
-
- //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();
- rabund = new RAbundVector();
- *rabund = (list->getRAbundVector());
-
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete list; delete rabund; globaldata->gListVector = NULL; return 0; }
-
- if(sorted) { rabund->print(out); }
- else { rabund->nonSortedPrint(out); }
-
- delete rabund;
- delete list;
- }
-
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); 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["rabund"].push_back(filename);
m->mothurOutEndLine();
out.close();
-
- globaldata->gListVector = NULL;
+
+ //set rabund file as new current rabundfile
+ string current = "";
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
return 0;
}
exit(1);
}
}
+//**********************************************************************************************************************
+int GetRAbundCommand::processList(ofstream& out){
+ try {
+ CountTable ct;
+ ct.readTable(countfile, false, 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);
+
+ if(sorted) { rabund->print(out); }
+ else { rabund->nonSortedPrint(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);
+
+ if(sorted) { rabund->print(out); }
+ else { rabund->nonSortedPrint(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);
+
+ if(sorted) { rabund->print(out); }
+ else { rabund->nonSortedPrint(out); }
+
+ delete rabund;
+ delete list;
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "processList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetRAbundCommand::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, "GetRAbundCommand", "createRabund");
+ exit(1);
+ }
+
+}
//**********************************************************************************************************************
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