--- /dev/null
+/*
+ * otuassociationcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 1/19/12.
+ * Copyright 2012 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "otuassociationcommand.h"
+#include "linearalgebra.h"
+
+//**********************************************************************************************************************
+vector<string> OTUAssociationCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
+ 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, "OTUAssociationCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string OTUAssociationCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The otu.association command reads a shared or relabund file and calculates the correlation coefficients between otus.\n";
+ helpString += "The otu.association command parameters are shared, relabund, groups, method and label. The shared or relabund parameter is required.\n";
+ helpString += "The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n";
+ helpString += "The label parameter allows you to select what distances level you would like used, and are also separated by dashes.\n";
+ helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n";
+ helpString += "The otu.association command should be in the following format: otu.association(shared=yourSharedFile, method=yourMethod).\n";
+ helpString += "Example otu.association(shared=genus.pool.shared, method=kendall).\n";
+ helpString += "The otu.association command outputs a .otu.corr 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, "OTUAssociationCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+OTUAssociationCommand::OTUAssociationCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["otu.corr"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "OTUAssociationCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+OTUAssociationCommand::OTUAssociationCommand(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();
+
+ 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["otu.corr"] = 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; }
+ }
+
+ 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
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { inputFileName = sharedfile; m->setSharedFile(sharedfile); }
+
+ relabundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relabundfile == "not open") { abort = true; }
+ else if (relabundfile == "not found") { relabundfile = ""; }
+ else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; pickedGroups = false; }
+ else {
+ pickedGroups = true;
+ m->splitAtDash(groups, Groups);
+ }
+ m->setGroups(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 = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ if ((relabundfile == "") && (sharedfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to shared, then relabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputFileName = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ relabundfile = m->getRelAbundFile();
+ if (relabundfile != "") { inputFileName = relabundfile; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You must provide either a shared or relabund file."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
+
+
+ if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("You may only use one of the following : shared or relabund file."); m->mothurOutEndLine(); abort = true; }
+
+ 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, "OTUAssociationCommand", "OTUAssociationCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int OTUAssociationCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //function are identical just different datatypes
+ if (sharedfile != "") { processShared(); }
+ else if (relabundfile != "") { processRelabund(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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, "OTUAssociationCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int OTUAssociationCommand::processShared(){
+ try {
+ InputData* input = new InputData(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> 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) { delete input; return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+ }
+
+ 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);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+ }
+
+ 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);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+ }
+
+ delete input;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "processShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int OTUAssociationCommand::process(vector<SharedRAbundVector*>& lookup){
+ try {
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr";
+ outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //column headings
+ out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n";
+
+ vector< vector<double> > xy; xy.resize(lookup[0]->getNumBins());
+ for (int i = 0; i < lookup[0]->getNumBins(); i++) { for (int j = 0; j < lookup.size(); j++) { xy[i].push_back(lookup[j]->getAbundance(i)); } }
+
+ LinearAlgebra linear;
+ for (int i = 0; i < xy.size(); i++) {
+
+ for (int k = 0; k < i; k++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ double coef = 0.0;
+ double sig = 0.0;
+ if (method == "spearman") { coef = linear.calcSpearman(xy[i], xy[k], sig); }
+ else if (method == "pearson") { coef = linear.calcPearson(xy[i], xy[k], sig); }
+ else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); }
+ else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << '\t' << coef << '\t' << sig << endl;
+ }
+ }
+
+ out.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int OTUAssociationCommand::processRelabund(){
+ try {
+ InputData* input = new InputData(relabundfile, "relabund");
+ vector<SharedRAbundFloatVector*> lookup = input->getSharedRAbundFloatVectors();
+ 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) { delete input; return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+ }
+
+ 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->getSharedRAbundFloatVectors(lastLabel);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+ }
+
+ 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->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 < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundFloatVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup);
+ }
+
+ delete input;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "processRelabund");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int OTUAssociationCommand::process(vector<SharedRAbundFloatVector*>& lookup){
+ try {
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + method + ".otu.corr";
+ outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //column headings
+ out << "OTUA\tOTUB\t" << method << "Coef\tSignificance\n";
+
+ vector< vector<double> > xy; xy.resize(lookup[0]->getNumBins());
+ for (int i = 0; i < lookup[0]->getNumBins(); i++) { for (int j = 0; j < lookup.size(); j++) { xy[i].push_back(lookup[j]->getAbundance(i)); } }
+
+ LinearAlgebra linear;
+ for (int i = 0; i < xy.size(); i++) {
+
+ for (int k = 0; k < i; k++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ double coef = 0.0;
+ double sig = 0.0;
+ if (method == "spearman") { coef = linear.calcSpearman(xy[i], xy[k], sig); }
+ else if (method == "pearson") { coef = linear.calcPearson(xy[i], xy[k], sig); }
+ else if (method == "kendall") { coef = linear.calcKendall(xy[i], xy[k], sig); }
+ else { m->mothurOut("[ERROR]: invalid method, choices are spearman, pearson or kendall."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ out << m->binLabelsInFile[i] << '\t' << m->binLabelsInFile[k] << coef << '\t' << sig << endl;
+ }
+ }
+
+ out.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OTUAssociationCommand", "process");
+ exit(1);
+ }
+}
+/*****************************************************************/
+
+
+
+
+
+
+
+
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