--- /dev/null
+/*
+ * getrelabundcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 6/21/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getrelabundcommand.h"
+
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "",false,false); parameters.push_back(pscale);
+ 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, "GetRelAbundCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetRelAbundCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.relabund command parameters are shared, groups, scale and label. shared is required, unless you have a valid current file.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
+ helpString += "The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n";
+ helpString += "The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n";
+ helpString += "Example get.relabund(groups=A-B-C, scale=averagegroup).\n";
+ helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
+ helpString += "The get.relabund command outputs a .relabund file.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetRelAbundCommand::GetRelAbundCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["relabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetRelAbundCommand::GetRelAbundCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //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();
+
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["relabund"] = tempOutNames;
+
+ //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("shared");
+ //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["shared"] = inputDir + it->second; }
+ }
+ }
+
+ //get shared file
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setSharedFile(sharedfile); }
+
+
+ //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(sharedfile); }
+
+ //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 {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; pickedGroups = false; }
+ else {
+ pickedGroups = true;
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
+ }
+
+ scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { 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;
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetRelAbundCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "relabund";
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ input = new InputData(sharedfile, "sharedfile");
+ lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->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;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+ getRelAbundance(lookup, out);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+ getRelAbundance(lookup, out);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ }
+
+ 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) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
+ }
+
+ if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ //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) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
+ getRelAbundance(lookup, out);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ //reset groups parameter
+ m->clearGroups();
+ delete input;
+ out.close();
+
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
+ m->mothurOutEndLine();
+
+ //set relabund file as new current relabundfile
+ string current = "";
+ itTypes = outputTypes.find("relabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRelAbundFile(current); }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
+ try {
+
+ 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");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
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