2 * getlistcountcommand.cpp
5 * Created by westcott on 10/12/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
10 #include "getlistcountcommand.h"
12 //**********************************************************************************************************************
13 vector<string> GetListCountCommand::setParameters(){
15 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otu",false,true, true); parameters.push_back(plist);
16 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
17 CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "","",false,false); parameters.push_back(parasort);
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, "GetListCountCommand", "setParameters");
30 //**********************************************************************************************************************
31 string GetListCountCommand::getHelpString(){
33 string helpString = "";
34 helpString += "The get.otulist command parameters are list, sort and label. list is required, unless you have a valid current list file.\n";
35 helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
36 helpString += "The sort parameter allows you to select how you want the output displayed. Options are otu and name.\n";
37 helpString += "If otu is selected the output will be otu number followed by the list of names in that otu.\n";
38 helpString += "If name is selected the output will be a sequence name followed by its otu number.\n";
39 helpString += "The get.otulist command should be in the following format: get.otulist(list=yourlistFile, label=yourLabels).\n";
40 helpString += "Example get.otulist(list=amazon.fn.list, label=0.10).\n";
41 helpString += "The default value for label is all lines in your inputfile.\n";
42 helpString += "The get.otulist command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n";
43 helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
47 m->errorOut(e, "GetListCountCommand", "getHelpString");
51 //**********************************************************************************************************************
52 string GetListCountCommand::getOutputPattern(string type) {
56 if (type == "otu") { pattern = "[filename],[tag],otu"; }
57 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
62 m->errorOut(e, "GetListCountCommand", "getOutputPattern");
66 //**********************************************************************************************************************
67 GetListCountCommand::GetListCountCommand(){
69 abort = true; calledHelp = true;
71 vector<string> tempOutNames;
72 outputTypes["otu"] = tempOutNames;
75 m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
79 //**********************************************************************************************************************
80 GetListCountCommand::GetListCountCommand(string option) {
82 abort = false; calledHelp = false;
85 //allow user to run help
86 if(option == "help") { help(); abort = true; calledHelp = true; }
87 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
90 vector<string> myArray = setParameters();
92 OptionParser parser(option);
93 map<string, string> parameters = parser.getParameters();
95 ValidParameters validParameter;
96 map<string, string>::iterator it;
98 //check to make sure all parameters are valid for command
99 for (it = parameters.begin(); it != parameters.end(); it++) {
100 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
103 //initialize outputTypes
104 vector<string> tempOutNames;
105 outputTypes["otu"] = tempOutNames;
107 //if the user changes the input directory command factory will send this info to us in the output parameter
108 string inputDir = validParameter.validFile(parameters, "inputdir", false);
109 if (inputDir == "not found"){ inputDir = ""; }
112 it = parameters.find("list");
113 //user has given a template file
114 if(it != parameters.end()){
115 path = m->hasPath(it->second);
116 //if the user has not given a path then, add inputdir. else leave path alone.
117 if (path == "") { parameters["list"] = inputDir + it->second; }
121 //if the user changes the output directory command factory will send this info to us in the output parameter
122 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
124 //check for required parameters
125 listfile = validParameter.validFile(parameters, "list", true);
126 if (listfile == "not found") {
127 listfile = m->getListFile();
128 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
129 else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
131 else if (listfile == "not open") { abort = true; }
132 else { m->setListFile(listfile); }
135 //check for optional parameter and set defaults
136 // ...at some point should added some additional type checking...
137 sort = validParameter.validFile(parameters, "sort", false); if (sort == "not found") { sort = "otu"; }
138 if ((sort != "otu") && (sort != "name")) { m->mothurOut( sort + " is not a valid sort option. Options are otu and name. I will use otu."); m->mothurOutEndLine(); sort = "otu"; }
140 label = validParameter.validFile(parameters, "label", false);
141 if (label == "not found") { label = ""; }
143 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
144 else { allLines = 1; }
148 catch(exception& e) {
149 m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
153 //**********************************************************************************************************************
155 int GetListCountCommand::execute(){
157 if (abort == true) { if (calledHelp) { return 0; } return 2; }
159 input = new InputData(listfile, "list");
160 list = input->getListVector();
161 string lastLabel = list->getLabel();
163 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
164 set<string> processedLabels;
165 set<string> userLabels = labels;
167 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
169 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
171 if(allLines == 1 || labels.count(list->getLabel()) == 1){
175 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
177 processedLabels.insert(list->getLabel());
178 userLabels.erase(list->getLabel());
181 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
182 string saveLabel = list->getLabel();
185 list = input->getListVector(lastLabel);
189 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
192 processedLabels.insert(list->getLabel());
193 userLabels.erase(list->getLabel());
195 //restore real lastlabel to save below
196 list->setLabel(saveLabel);
199 lastLabel = list->getLabel();
202 list = input->getListVector();
206 //output error messages about any remaining user labels
207 set<string>::iterator it;
208 bool needToRun = false;
209 for (it = userLabels.begin(); it != userLabels.end(); it++) {
210 m->mothurOut("Your file does not include the label " + *it);
211 if (processedLabels.count(lastLabel) != 1) {
212 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
215 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
219 //run last label if you need to
220 if (needToRun == true) {
221 if (list != NULL) { delete list; }
222 list = input->getListVector(lastLabel);
226 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
233 m->mothurOutEndLine();
234 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
235 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
236 m->mothurOutEndLine();
240 catch(exception& e) {
241 m->errorOut(e, "GetListCountCommand", "execute");
246 //**********************************************************************************************************************
247 //return 1 if error, 0 otherwise
248 void GetListCountCommand::process(ListVector* list) {
251 if (outputDir == "") { outputDir += m->hasPath(listfile); }
252 map<string, string> variables;
253 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
254 variables["[tag]"] = list->getLabel();
255 string outputFileName = getOutputFileName("otu", variables);
257 m->openOutputFile(outputFileName, out);
258 outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
260 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
262 //for each bin in the list vector
263 for (int i = 0; i < list->getNumBins(); i++) {
264 if (m->control_pressed) { break; }
266 binnames = list->get(i);
269 out << i+1 << '\t' << binnames << endl;
271 vector<string> names;
272 m->splitAtComma(binnames, names);
274 for (int j = 0; j < names.size(); j++) {
275 out << names[j] << '\t' << i+1 << endl;
282 catch(exception& e) {
283 m->errorOut(e, "GetListCountCommand", "process");
287 //**********************************************************************************************************************