--- /dev/null
+/*
+ * corraxescommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 12/22/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "corraxescommand.h"
+
+//**********************************************************************************************************************
+vector<string> CorrAxesCommand::getValidParameters(){
+ try {
+ string Array[] = {"axes","shared","relabund","numaxes","label","groups","method","metastats","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CorrAxesCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"axes"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CorrAxesCommand::CorrAxesCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["corr.axes"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "CorrAxesCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+vector<string> CorrAxesCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CorrAxesCommand::CorrAxesCommand(string option) {
+ try {
+ abort = false;
+ globaldata = GlobalData::getInstance();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"axes","shared","relabund","numaxes","label","groups","method","metastats","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //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; }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["corr.axes"] = 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("axes");
+ //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["axes"] = inputDir + it->second; }
+ }
+
+ 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; }
+ }
+
+ it = parameters.find("relabund");
+ //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["relabund"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ axesfile = validParameter.validFile(parameters, "axes", true);
+ if (axesfile == "not open") { abort = true; }
+ else if (axesfile == "not found") { axesfile = ""; m->mothurOut("axes is a required parameter for the corr.axes command."); m->mothurOutEndLine(); abort = true; }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { inputFileName = sharedfile; }
+
+ relabundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relabundfile == "not open") { abort = true; }
+ else if (relabundfile == "not found") { relabundfile = ""; }
+ else { inputFileName = relabundfile; }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; pickedGroups = false; }
+ else {
+ pickedGroups = true;
+ m->splitAtDash(groups, Groups);
+ }
+ globaldata->Groups = Groups;
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputFileName); }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
+
+ if ((relabundfile == "") && (sharedfile == "")) { m->mothurOut("You must provide either a shared or relabund file."); m->mothurOutEndLine(); abort = true; }
+
+ if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true; }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "numaxes", false); if (temp == "not found"){ temp = "3"; }
+ convert(temp, numaxes);
+
+ method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "pearson"; }
+
+ if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "CorrAxesCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void CorrAxesCommand::help(){
+ try {
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+CorrAxesCommand::~CorrAxesCommand(){}
+
+//**********************************************************************************************************************
+
+int CorrAxesCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ /*************************************************************************************/
+ // use smart distancing to get right sharedRabund and convert to relabund if needed //
+ /************************************************************************************/
+ if (sharedfile != "") {
+ getShared();
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+ if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
+
+ //fills lookupFloat with relative abundance values from lookup
+ convertToRelabund();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }else {
+ getSharedFloat();
+ if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+ if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
+
+ if (pickedGroups) { eliminateZeroOTUS(lookupFloat); }
+ }
+
+ if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+
+ //this is for a sanity check to make sure the axes file and shared file match
+ for (int i = 0; i < lookupFloat.size(); i++) { names.insert(lookupFloat[i]->getGroup()); }
+
+ /*************************************************************************************/
+ // read axes file and check for file mismatches with shared or relabund file //
+ /************************************************************************************/
+
+ //read axes file
+ map<string, vector<float> > axes = readAxes();
+
+ if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+
+ //sanity check, the read only adds groups that are in the shared or relabund file, but we want to make sure the axes file isn't missing anyone
+ if (axes.size() != lookupFloat.size()) {
+ map<string, vector<float> >::iterator it;
+ for (int i = 0; i < lookupFloat.size(); i++) {
+ it = axes.find(lookupFloat[i]->getGroup());
+ if (it == axes.end()) { m->mothurOut(lookupFloat[i]->getGroup() + " is in your shared of relabund file but not in your axes file, please correct."); m->mothurOutEndLine(); }
+ }
+ m->control_pressed = true;
+ }
+
+ if (m->control_pressed) { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + "corr.axes";
+ outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ if (method == "pearson") { calcPearson(axes, out); }
+ //else if (method == "spearman") { calcSpearman(axes, out); }
+ //else if (method == "kendall") { calcKendal(axes, out); }
+ //else { m->mothurOut("[ERROR]: Invalid method."); m->mothurOutEndLine(); }
+
+ out.close();
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int CorrAxesCommand::calcPearson(map<string, vector<float> >& axes, ofstream& out) {
+ try {
+
+ //find average of each axis - X
+ vector<float> averageAxes; averageAxes.resize(numaxes, 0.0);
+ for (map<string, vector<float> >::iterator it = axes.begin(); it != axes.end(); it++) {
+ vector<float> temp = it->second;
+ for (int i = 0; i < temp.size(); i++) {
+ averageAxes[i] += temp[i];
+ }
+ }
+
+ for (int i = 0; i < averageAxes.size(); i++) { averageAxes[i] = averageAxes[i] / (float) axes.size(); }
+
+ //for each otu
+ for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
+
+ //find the averages this otu - Y
+ float sumOtu = 0.0;
+ for (int j = 0; j < lookupFloat.size(); j++) {
+ sumOtu += lookupFloat[j]->getAbundance(i);
+ }
+ float Ybar = sumOtu / (float) lookupFloat.size();
+
+ //find the average
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "calcPearson");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int CorrAxesCommand::getShared(){
+ try {
+ InputData* input = new InputData(sharedfile, "sharedfile");
+ lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ if (label == "") { label = lastLabel; delete input; return 0; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(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) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { delete input; return 0; }
+
+ if(labels.count(lookup[0]->getLabel()) == 1){
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ break;
+ }
+
+ 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);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors();
+ }
+
+
+ if (m->control_pressed) { delete input; 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);
+ }
+
+ delete input;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "getShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int CorrAxesCommand::getSharedFloat(){
+ try {
+ InputData* input = new InputData(relabundfile, "relabund");
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ string lastLabel = lookupFloat[0]->getLabel();
+
+ if (label == "") { label = lastLabel; delete input; return 0; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> labels; labels.insert(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((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
+
+ if (m->control_pressed) { delete input; return 0; }
+
+ if(labels.count(lookupFloat[0]->getLabel()) == 1){
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookupFloat[0]->getLabel();
+
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookupFloat[0]->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = lookupFloat[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ }
+
+
+ if (m->control_pressed) { delete input; 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 < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+ }
+
+ delete input;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "getSharedFloat");
+ exit(1);
+ }
+}
+/*****************************************************************/
+int CorrAxesCommand::convertToRelabund(){
+ try {
+
+ vector<SharedRAbundFloatVector*> newLookup;
+ for (int i = 0; i < lookup.size(); i++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(lookup[i]->getLabel());
+ temp->setGroup(lookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ for (int i = 0; i < lookup.size(); i++) {
+
+ for (int j = 0; j < lookup[i]->getNumBins(); j++) {
+
+ if (m->control_pressed) { return 0; }
+
+ int abund = lookup[i]->getAbundance(j);
+
+ float relabund = abund / (float) lookup[i]->getNumSeqs();
+
+ newLookup[i]->push_back(relabund, lookup[i]->getGroup());
+ }
+ }
+
+ if (pickedGroups) { eliminateZeroOTUS(newLookup); }
+
+ lookupFloat = newLookup;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "convertToRelabund");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundFloatVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundFloatVector* temp = new SharedRAbundFloatVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+
+ thislookup = newLookup;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
+/*****************************************************************/
+map<string, vector<float> > CorrAxesCommand::readAxes(){
+ try {
+ map<string, vector<float> > axes;
+
+ ifstream in;
+ m->openInputFile(axesfile, in);
+
+ string headerLine = m->getline(in); m->gobble(in);
+
+ //count the number of axis you are reading
+ bool done = false;
+ int count = 0;
+ while (!done) {
+ int pos = headerLine.find("axis");
+ if (pos != string::npos) {
+ count++;
+ headerLine = headerLine.substr(pos+4);
+ }else { done = true; }
+ }
+ cout << "count = " << count << endl;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return axes; }
+
+ string group = "";
+ in >> group; m->gobble(in);
+
+ vector<float> thisGroupsAxes;
+ for (int i = 0; i < count; i++) {
+ float temp = 0.0;
+ in >> temp;
+
+ //only save the axis we want
+ if (i < numaxes) { thisGroupsAxes.push_back(temp); }
+ }
+
+ //save group if its one the user selected
+ if (names.count(group) != 0) {
+ map<string, vector<float> >::iterator it = axes.find(group);
+
+ if (it == axes.end()) {
+ axes[group] = thisGroupsAxes;
+ }else {
+ m->mothurOut(group + " is already in your axes file, using first definition."); m->mothurOutEndLine();
+ }
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+
+ return axes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CorrAxesCommand", "convertToRelabund");
+ exit(1);
+ }
+}
+/*****************************************************************/
+
+
+
+
+
+
projects / mothur.git / commitdiff