2 // getotulabelscommand.cpp
5 // Created by Sarah Westcott on 5/21/12.
6 // Copyright (c) 2012 Schloss Lab. All rights reserved.
9 #include "getotulabelscommand.h"
11 //**********************************************************************************************************************
12 vector<string> GetOtuLabelsCommand::setParameters(){
14 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true, true); parameters.push_back(paccnos);
15 CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false, true); parameters.push_back(pconstaxonomy);
16 CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false, true); parameters.push_back(potucorr);
17 CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false, true); parameters.push_back(pcorraxes);
18 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
19 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
21 vector<string> myArray;
22 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
26 m->errorOut(e, "GetOtuLabelsCommand", "setParameters");
30 //**********************************************************************************************************************
31 string GetOtuLabelsCommand::getHelpString(){
33 string helpString = "";
34 helpString += "The get.otulabels command can be used to select specific otus with the output from classify.otu, otu.association, or corr.axes.\n";
35 helpString += "The get.otulabels parameters are: constaxonomy, otucorr, corraxes, and accnos.\n";
36 helpString += "The constaxonomy parameter is used to input the results of the classify.otu command.\n";
37 helpString += "The otucorr parameter is used to input the results of the otu.association command.\n";
38 helpString += "The corraxes parameter is used to input the results of the corr.axes command.\n";
39 helpString += "The get.otulabels commmand should be in the following format: \n";
40 helpString += "get.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n";
44 m->errorOut(e, "GetOtuLabelsCommand", "getHelpString");
48 //**********************************************************************************************************************
49 string GetOtuLabelsCommand::getOutputPattern(string type) {
53 if (type == "constaxonomy") { pattern = "[filename],pick,[extension]"; }
54 else if (type == "otucorr") { pattern = "[filename],pick,[extension]"; }
55 else if (type == "corraxes") { pattern = "[filename],pick,[extension]"; }
56 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
61 m->errorOut(e, "GetOtuLabelsCommand", "getOutputPattern");
66 //**********************************************************************************************************************
67 GetOtuLabelsCommand::GetOtuLabelsCommand(){
69 abort = true; calledHelp = true;
71 vector<string> tempOutNames;
72 outputTypes["constaxonomy"] = tempOutNames;
73 outputTypes["otucorr"] = tempOutNames;
74 outputTypes["corraxes"] = tempOutNames;
77 m->errorOut(e, "GetOtuLabelsCommand", "GetOtuLabelsCommand");
81 //**********************************************************************************************************************
82 GetOtuLabelsCommand::GetOtuLabelsCommand(string option) {
84 abort = false; calledHelp = false;
86 //allow user to run help
87 if(option == "help") { help(); abort = true; calledHelp = true; }
88 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
91 //valid paramters for this command
92 vector<string> myArray = setParameters();
94 OptionParser parser(option);
95 map<string,string> parameters = parser.getParameters();
97 ValidParameters validParameter;
98 map<string,string>::iterator it;
99 //check to make sure all parameters are valid for command
100 for (it = parameters.begin(); it != parameters.end(); it++) {
101 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
105 //if the user changes the input directory command factory will send this info to us in the output parameter
106 string inputDir = validParameter.validFile(parameters, "inputdir", false);
107 if (inputDir == "not found"){ inputDir = ""; }
110 //edit file types below to include only the types you added as parameters
113 it = parameters.find("constaxonomy");
114 //user has given a template file
115 if(it != parameters.end()){
116 path = m->hasPath(it->second);
117 //if the user has not given a path then, add inputdir. else leave path alone.
118 if (path == "") { parameters["constaxonomy"] = inputDir + it->second; }
121 it = parameters.find("accnos");
122 //user has given a template file
123 if(it != parameters.end()){
124 path = m->hasPath(it->second);
125 //if the user has not given a path then, add inputdir. else leave path alone.
126 if (path == "") { parameters["accnos"] = inputDir + it->second; }
129 it = parameters.find("corraxes");
130 //user has given a template file
131 if(it != parameters.end()){
132 path = m->hasPath(it->second);
133 //if the user has not given a path then, add inputdir. else leave path alone.
134 if (path == "") { parameters["corraxes"] = inputDir + it->second; }
137 it = parameters.find("otucorr");
138 //user has given a template file
139 if(it != parameters.end()){
140 path = m->hasPath(it->second);
141 //if the user has not given a path then, add inputdir. else leave path alone.
142 if (path == "") { parameters["otucorr"] = inputDir + it->second; }
146 vector<string> tempOutNames;
147 outputTypes["constaxonomy"] = tempOutNames;
148 outputTypes["otucorr"] = tempOutNames;
149 outputTypes["corraxes"] = tempOutNames;
151 //check for parameters
152 accnosfile = validParameter.validFile(parameters, "accnos", true);
153 if (accnosfile == "not open") { abort = true; }
154 else if (accnosfile == "not found") {
155 accnosfile = m->getAccnosFile();
156 if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
158 m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
161 }else { m->setAccnosFile(accnosfile); }
163 constaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true);
164 if (constaxonomyfile == "not open") { constaxonomyfile = ""; abort = true; }
165 else if (constaxonomyfile == "not found") { constaxonomyfile = ""; }
167 corraxesfile = validParameter.validFile(parameters, "corraxes", true);
168 if (corraxesfile == "not open") { corraxesfile = ""; abort = true; }
169 else if (corraxesfile == "not found") { corraxesfile = ""; }
171 otucorrfile = validParameter.validFile(parameters, "otucorr", true);
172 if (otucorrfile == "not open") { otucorrfile = ""; abort = true; }
173 else if (otucorrfile == "not found") { otucorrfile = ""; }
176 //if the user changes the output directory command factory will send this info to us in the output parameter
177 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
179 if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == "")) { m->mothurOut("You must provide one of the following: constaxonomy, corraxes or otucorr."); m->mothurOutEndLine(); abort = true; }
183 catch(exception& e) {
184 m->errorOut(e, "GetOtuLabelsCommand", "GetOtuLabelsCommand");
188 //**********************************************************************************************************************
190 int GetOtuLabelsCommand::execute(){
193 if (abort == true) { if (calledHelp) { return 0; } return 2; }
195 //get labels you want to keep
196 labels = m->readAccnos(accnosfile);
198 if (m->control_pressed) { return 0; }
200 //read through the correct file and output lines you want to keep
201 if (constaxonomyfile != "") { readClassifyOtu(); }
202 if (corraxesfile != "") { readCorrAxes(); }
203 if (otucorrfile != "") { readOtuAssociation(); }
205 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
207 //output files created by command
208 m->mothurOutEndLine();
209 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
210 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
211 m->mothurOutEndLine();
215 catch(exception& e) {
216 m->errorOut(e, "GetOtuLabelsCommand", "execute");
220 //**********************************************************************************************************************
221 int GetOtuLabelsCommand::readClassifyOtu(){
223 string thisOutputDir = outputDir;
224 if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); }
225 map<string, string> variables;
226 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
227 variables["[extension]"] = m->getExtension(constaxonomyfile);
228 string outputFileName = getOutputFileName("constaxonomy", variables);
231 m->openOutputFile(outputFileName, out);
234 m->openInputFile(constaxonomyfile, in);
236 bool wroteSomething = false;
237 int selectedCount = 0;
240 string headers = m->getline(in);
241 out << headers << endl;
245 if (m->control_pressed) { break; }
247 string otu = ""; string tax = "unknown";
250 in >> otu >> size >> tax; m->gobble(in);
252 if (labels.count(otu) != 0) {
253 wroteSomething = true;
256 out << otu << '\t' << size << '\t' << tax << endl;
262 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); }
263 outputNames.push_back(outputFileName); outputTypes["constaxonomy"].push_back(outputFileName);
265 m->mothurOut("Selected " + toString(selectedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
270 catch(exception& e) {
271 m->errorOut(e, "GetOtuLabelsCommand", "readClassifyOtu");
275 //**********************************************************************************************************************
276 int GetOtuLabelsCommand::readOtuAssociation(){
278 string thisOutputDir = outputDir;
279 if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); }
280 map<string, string> variables;
281 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
282 variables["[extension]"] = m->getExtension(otucorrfile);
283 string outputFileName = getOutputFileName("otucorr", variables);
286 m->openOutputFile(outputFileName, out);
289 m->openInputFile(otucorrfile, in);
291 bool wroteSomething = false;
292 int selectedCount = 0;
295 string headers = m->getline(in);
296 out << headers << endl;
300 if (m->control_pressed) { break; }
305 string line = m->getline(in); m->gobble(in);
307 if ((labels.count(otu1) != 0) && (labels.count(otu2) != 0)){
308 wroteSomething = true;
311 out << otu1 << '\t' << otu2 << '\t' << line << endl;
317 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); }
318 outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
320 m->mothurOut("Selected " + toString(selectedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
325 catch(exception& e) {
326 m->errorOut(e, "GetOtuLabelsCommand", "readOtuAssociation");
330 //**********************************************************************************************************************
331 int GetOtuLabelsCommand::readCorrAxes(){
333 string thisOutputDir = outputDir;
334 if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); }
335 map<string, string> variables;
336 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
337 variables["[extension]"] = m->getExtension(corraxesfile);
338 string outputFileName = getOutputFileName("corraxes", variables);
341 m->openOutputFile(outputFileName, out);
345 m->openInputFile(corraxesfile, in);
347 bool wroteSomething = false;
348 int selectedCount = 0;
351 string headers = m->getline(in);
352 out << headers << endl;
356 if (m->control_pressed) { break; }
360 string line = m->getline(in); m->gobble(in);
362 if (labels.count(otu) != 0) {
363 wroteSomething = true;
366 out << otu << '\t' << line << endl;
372 if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); }
373 outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName);
375 m->mothurOut("Selected " + toString(selectedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
380 catch(exception& e) {
381 m->errorOut(e, "GetOtuLabelsCommand", "readCorrAxes");
385 //**********************************************************************************************************************