--- /dev/null
+//
+// getotulabelscommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 5/21/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "getotulabelscommand.h"
+
+//**********************************************************************************************************************
+vector<string> GetOtuLabelsCommand::setParameters(){
+ try {
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
+ CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
+ CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
+ CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes);
+ 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, "GetOtuLabelsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetOtuLabelsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.otulabels command can be used to select specific otus with the output from classify.otu, otu.association, or corr.axes.\n";
+ helpString += "The get.otulabels parameters are: constaxonomy, otucorr, corraxes, and accnos.\n";
+ helpString += "The constaxonomy parameter is input the results of the classify.otu command.\n";
+ helpString += "The otucorr parameter is input the results of the otu.association command.\n";
+ helpString += "The corraxes parameter is input the results of the corr.axes command.\n";
+ helpString += "The get.otulabels commmand should be in the following format: \n";
+ helpString += "get.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtuLabelsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetOtuLabelsCommand::GetOtuLabelsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["contaxonomy"] = tempOutNames;
+ outputTypes["otu.corr"] = tempOutNames;
+ outputTypes["corr.axes"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtuLabelsCommand", "GetOtuLabelsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetOtuLabelsCommand::GetOtuLabelsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //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
+ 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; }
+ }
+
+
+ //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 {
+
+ //edit file types below to include only the types you added as parameters
+
+ string path;
+ it = parameters.find("constaxonomy");
+ //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["constaxonomy"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("accnos");
+ //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["accnos"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("corraxes");
+ //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["corraxes"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("otucorr");
+ //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["otucorr"] = inputDir + it->second; }
+ }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["contaxonomy"] = tempOutNames;
+ outputTypes["otu.corr"] = tempOutNames;
+ outputTypes["corr.axes"] = tempOutNames;
+
+ //check for parameters
+ accnosfile = validParameter.validFile(parameters, "accnos", true);
+ if (accnosfile == "not open") { abort = true; }
+ else if (accnosfile == "not found") {
+ accnosfile = m->getAccnosFile();
+ if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { m->setAccnosFile(accnosfile); }
+
+ constaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true);
+ if (constaxonomyfile == "not open") { constaxonomyfile = ""; abort = true; }
+ else if (constaxonomyfile == "not found") { constaxonomyfile = ""; }
+
+ corraxesfile = validParameter.validFile(parameters, "corraxes", true);
+ if (corraxesfile == "not open") { corraxesfile = ""; abort = true; }
+ else if (corraxesfile == "not found") { corraxesfile = ""; }
+
+ otucorrfile = validParameter.validFile(parameters, "otucorr", true);
+ if (otucorrfile == "not open") { otucorrfile = ""; abort = true; }
+ else if (otucorrfile == "not found") { otucorrfile = ""; }
+
+
+ //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 = ""; }
+
+ if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == "")) { m->mothurOut("You must provide one of the following: constaxonomy, corraxes or otucorr."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtuLabelsCommand", "GetOtuLabelsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetOtuLabelsCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //get labels you want to keep
+ readAccnos();
+
+ if (m->control_pressed) { return 0; }
+
+ //read through the correct file and output lines you want to keep
+ if (constaxonomyfile != "") { readClassifyOtu(); }
+ if (corraxesfile != "") { readCorrAxes(); }
+ if (otucorrfile != "") { readOtuAssociation(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //output files created by command
+ 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, "GetOtuLabelsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetOtuLabelsCommand::readClassifyOtu(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + "pick.taxonomy";
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(constaxonomyfile, in);
+
+ bool wroteSomething = false;
+ int selectedCount = 0;
+
+ //read headers
+ string headers = m->getline(in);
+ out << headers << endl;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ string otu = ""; string tax = "unknown";
+ int size = 0;
+
+ in >> otu >> size >> tax; m->gobble(in);
+
+ if (labels.count(otu) != 0) {
+ wroteSomething = true;
+ selectedCount++;
+
+ out << otu << '\t' << size << '\t' << tax << endl;
+ }
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["constaxonomy"].push_back(outputFileName);
+
+ m->mothurOut("Selected " + toString(selectedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtuLabelsCommand", "readClassifyOtu");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetOtuLabelsCommand::readOtuAssociation(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + "pick.corr";
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(otucorrfile, in);
+
+ bool wroteSomething = false;
+ int selectedCount = 0;
+
+ //read headers
+ string headers = m->getline(in);
+ out << headers << endl;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ string otu1 = "";
+ string otu2 = "";
+ in >> otu1 >> otu2;
+ string line = m->getline(in); m->gobble(in);
+
+ if ((labels.count(otu1) != 0) && (labels.count(otu2) != 0)){
+ wroteSomething = true;
+ selectedCount++;
+
+ out << otu1 << '\t' << otu2 << '\t' << line << endl;
+ }
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["otu.corr"].push_back(outputFileName);
+
+ m->mothurOut("Selected " + toString(selectedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtuLabelsCommand", "readOtuAssociation");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetOtuLabelsCommand::readCorrAxes(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + "pick.axes";
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(corraxesfile, in);
+
+ bool wroteSomething = false;
+ int selectedCount = 0;
+
+ //read headers
+ string headers = m->getline(in);
+ out << headers << endl;
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ string otu = "";
+ in >> otu;
+ string line = m->getline(in); m->gobble(in);
+
+ if (labels.count(otu) != 0) {
+ wroteSomething = true;
+ selectedCount++;
+
+ out << otu << '\t' << line << endl;
+ }
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName);
+
+ m->mothurOut("Selected " + toString(selectedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtuLabelsCommand", "readCorrAxes");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetOtuLabelsCommand::readAccnos(){
+ try {
+
+ ifstream in;
+ m->openInputFile(accnosfile, in);
+ string name;
+
+ while(!in.eof()){
+ in >> name;
+
+ labels.insert(name);
+
+ m->gobble(in);
+ }
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOtuLabelsCommand", "readAccnos");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
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