5 // Created by Sarah Westcott on 5/21/12.
6 // Copyright (c) 2012 Schloss Lab. All rights reserved.
9 #include "removeotulabelscommand.h"
11 //**********************************************************************************************************************
12 vector<string> RemoveOtuLabelsCommand::setParameters(){
14 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
15 CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
16 CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
17 CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); 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, "RemoveOtuLabelsCommand", "setParameters");
30 //**********************************************************************************************************************
31 string RemoveOtuLabelsCommand::getHelpString(){
33 string helpString = "";
34 helpString += "The remove.otulabels command can be used to remove specific otus with the output from classify.otu, otu.association, or corr.axes.\n";
35 helpString += "The remove.otulabels parameters are: constaxonomy, otucorr, corraxes, and accnos.\n";
36 helpString += "The constaxonomy parameter is input the results of the classify.otu command.\n";
37 helpString += "The otucorr parameter is input the results of the otu.association command.\n";
38 helpString += "The corraxes parameter is input the results of the corr.axes command.\n";
39 helpString += "The remove.otulabels commmand should be in the following format: \n";
40 helpString += "remove.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n";
44 m->errorOut(e, "RemoveOtuLabelsCommand", "getHelpString");
48 //**********************************************************************************************************************
49 string RemoveOtuLabelsCommand::getOutputFileNameTag(string type, string inputName=""){
51 string outputFileName = "";
52 map<string, vector<string> >::iterator it;
54 //is this a type this command creates
55 it = outputTypes.find(type);
56 if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
58 if (type == "constaxonomy") { outputFileName = "pick.taxonomy"; }
59 else if (type == "otucorr") { outputFileName = "pick.corr"; }
60 else if (type == "corraxes") { outputFileName = "pick.axes"; }
61 else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
63 return outputFileName;
66 m->errorOut(e, "RemoveOtuLabelsCommand", "getOutputFileNameTag");
70 //**********************************************************************************************************************
71 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
73 abort = true; calledHelp = true;
75 vector<string> tempOutNames;
76 outputTypes["contaxonomy"] = tempOutNames;
77 outputTypes["otucorr"] = tempOutNames;
78 outputTypes["corraxes"] = tempOutNames;
81 m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
85 //**********************************************************************************************************************
86 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(string option) {
88 abort = false; calledHelp = false;
90 //allow user to run help
91 if(option == "help") { help(); abort = true; calledHelp = true; }
92 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
95 //valid paramters for this command
96 vector<string> myArray = setParameters();
98 OptionParser parser(option);
99 map<string,string> parameters = parser.getParameters();
101 ValidParameters validParameter;
102 map<string,string>::iterator it;
103 //check to make sure all parameters are valid for command
104 for (it = parameters.begin(); it != parameters.end(); it++) {
105 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
109 //if the user changes the input directory command factory will send this info to us in the output parameter
110 string inputDir = validParameter.validFile(parameters, "inputdir", false);
111 if (inputDir == "not found"){ inputDir = ""; }
114 //edit file types below to include only the types you added as parameters
117 it = parameters.find("constaxonomy");
118 //user has given a template file
119 if(it != parameters.end()){
120 path = m->hasPath(it->second);
121 //if the user has not given a path then, add inputdir. else leave path alone.
122 if (path == "") { parameters["constaxonomy"] = inputDir + it->second; }
125 it = parameters.find("accnos");
126 //user has given a template file
127 if(it != parameters.end()){
128 path = m->hasPath(it->second);
129 //if the user has not given a path then, add inputdir. else leave path alone.
130 if (path == "") { parameters["accnos"] = inputDir + it->second; }
133 it = parameters.find("corraxes");
134 //user has given a template file
135 if(it != parameters.end()){
136 path = m->hasPath(it->second);
137 //if the user has not given a path then, add inputdir. else leave path alone.
138 if (path == "") { parameters["corraxes"] = inputDir + it->second; }
141 it = parameters.find("otucorr");
142 //user has given a template file
143 if(it != parameters.end()){
144 path = m->hasPath(it->second);
145 //if the user has not given a path then, add inputdir. else leave path alone.
146 if (path == "") { parameters["otucorr"] = inputDir + it->second; }
150 vector<string> tempOutNames;
151 outputTypes["constaxonomy"] = tempOutNames;
152 outputTypes["otucorr"] = tempOutNames;
153 outputTypes["corraxes"] = tempOutNames;
155 //check for parameters
156 accnosfile = validParameter.validFile(parameters, "accnos", true);
157 if (accnosfile == "not open") { abort = true; }
158 else if (accnosfile == "not found") {
159 accnosfile = m->getAccnosFile();
160 if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
162 m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
165 }else { m->setAccnosFile(accnosfile); }
167 constaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true);
168 if (constaxonomyfile == "not open") { constaxonomyfile = ""; abort = true; }
169 else if (constaxonomyfile == "not found") { constaxonomyfile = ""; }
171 corraxesfile = validParameter.validFile(parameters, "corraxes", true);
172 if (corraxesfile == "not open") { corraxesfile = ""; abort = true; }
173 else if (corraxesfile == "not found") { corraxesfile = ""; }
175 otucorrfile = validParameter.validFile(parameters, "otucorr", true);
176 if (otucorrfile == "not open") { otucorrfile = ""; abort = true; }
177 else if (otucorrfile == "not found") { otucorrfile = ""; }
180 //if the user changes the output directory command factory will send this info to us in the output parameter
181 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
183 if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == "")) { m->mothurOut("You must provide one of the following: constaxonomy, corraxes or otucorr."); m->mothurOutEndLine(); abort = true; }
187 catch(exception& e) {
188 m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
192 //**********************************************************************************************************************
194 int RemoveOtuLabelsCommand::execute(){
197 if (abort == true) { if (calledHelp) { return 0; } return 2; }
199 //get labels you want to keep
200 labels = m->readAccnos(accnosfile);
202 if (m->control_pressed) { return 0; }
204 //read through the correct file and output lines you want to keep
205 if (constaxonomyfile != "") { readClassifyOtu(); }
206 if (corraxesfile != "") { readCorrAxes(); }
207 if (otucorrfile != "") { readOtuAssociation(); }
209 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
211 //output files created by command
212 m->mothurOutEndLine();
213 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
214 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
215 m->mothurOutEndLine();
219 catch(exception& e) {
220 m->errorOut(e, "GetOtuLabelsCommand", "execute");
224 //**********************************************************************************************************************
225 int RemoveOtuLabelsCommand::readClassifyOtu(){
227 string thisOutputDir = outputDir;
228 if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); }
229 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + getOutputFileNameTag("constaxonomy");
231 m->openOutputFile(outputFileName, out);
234 m->openInputFile(constaxonomyfile, in);
236 bool wroteSomething = false;
237 int removedCount = 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;
254 out << otu << '\t' << size << '\t' << tax << endl;
255 }else { removedCount++; }
260 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine(); }
261 outputNames.push_back(outputFileName); outputTypes["constaxonomy"].push_back(outputFileName);
263 m->mothurOut("Removed " + toString(removedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
268 catch(exception& e) {
269 m->errorOut(e, "RemoveOtuLabelsCommand", "readClassifyOtu");
273 //**********************************************************************************************************************
274 int RemoveOtuLabelsCommand::readOtuAssociation(){
276 string thisOutputDir = outputDir;
277 if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); }
278 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + getOutputFileNameTag("otucorr");
280 m->openOutputFile(outputFileName, out);
283 m->openInputFile(otucorrfile, in);
285 bool wroteSomething = false;
286 int removedCount = 0;
289 string headers = m->getline(in);
290 out << headers << endl;
294 if (m->control_pressed) { break; }
299 string line = m->getline(in); m->gobble(in);
301 if ((labels.count(otu1) == 0) && (labels.count(otu2) == 0)){
302 wroteSomething = true;
304 out << otu1 << '\t' << otu2 << '\t' << line << endl;
305 }else { removedCount++; }
310 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine(); }
311 outputNames.push_back(outputFileName); outputTypes["otucorr"].push_back(outputFileName);
313 m->mothurOut("Removed " + toString(removedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
318 catch(exception& e) {
319 m->errorOut(e, "RemoveOtuLabelsCommand", "readOtuAssociation");
323 //**********************************************************************************************************************
324 int RemoveOtuLabelsCommand::readCorrAxes(){
326 string thisOutputDir = outputDir;
327 if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); }
328 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + getOutputFileNameTag("corraxes");
330 m->openOutputFile(outputFileName, out);
334 m->openInputFile(corraxesfile, in);
336 bool wroteSomething = false;
337 int removedCount = 0;
340 string headers = m->getline(in);
341 out << headers << endl;
345 if (m->control_pressed) { break; }
349 string line = m->getline(in); m->gobble(in);
351 if (labels.count(otu) == 0) {
352 wroteSomething = true;
354 out << otu << '\t' << line << endl;
355 }else { removedCount++; }
360 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine(); }
361 outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName);
363 m->mothurOut("Removed " + toString(removedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
368 catch(exception& e) {
369 m->errorOut(e, "RemoveOtuLabelsCommand", "readCorrAxes");
373 //**********************************************************************************************************************