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",false,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 GetListCountCommand::GetListCountCommand(){
54 abort = true; calledHelp = true;
56 vector<string> tempOutNames;
57 outputTypes["otu"] = tempOutNames;
60 m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
64 //**********************************************************************************************************************
65 GetListCountCommand::GetListCountCommand(string option) {
67 abort = false; calledHelp = false;
70 //allow user to run help
71 if(option == "help") { help(); abort = true; calledHelp = true; }
72 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
75 vector<string> myArray = setParameters();
77 OptionParser parser(option);
78 map<string, string> parameters = parser.getParameters();
80 ValidParameters validParameter;
81 map<string, string>::iterator it;
83 //check to make sure all parameters are valid for command
84 for (it = parameters.begin(); it != parameters.end(); it++) {
85 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
88 //initialize outputTypes
89 vector<string> tempOutNames;
90 outputTypes["otu"] = tempOutNames;
92 //if the user changes the input directory command factory will send this info to us in the output parameter
93 string inputDir = validParameter.validFile(parameters, "inputdir", false);
94 if (inputDir == "not found"){ inputDir = ""; }
97 it = parameters.find("list");
98 //user has given a template file
99 if(it != parameters.end()){
100 path = m->hasPath(it->second);
101 //if the user has not given a path then, add inputdir. else leave path alone.
102 if (path == "") { parameters["list"] = inputDir + it->second; }
106 //if the user changes the output directory command factory will send this info to us in the output parameter
107 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
109 //check for required parameters
110 listfile = validParameter.validFile(parameters, "list", true);
111 if (listfile == "not found") {
112 listfile = m->getListFile();
113 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
114 else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
116 else if (listfile == "not open") { abort = true; }
117 else { m->setListFile(listfile); }
120 //check for optional parameter and set defaults
121 // ...at some point should added some additional type checking...
122 sort = validParameter.validFile(parameters, "sort", false); if (sort == "not found") { sort = "otu"; }
123 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"; }
125 label = validParameter.validFile(parameters, "label", false);
126 if (label == "not found") { label = ""; }
128 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
129 else { allLines = 1; }
133 catch(exception& e) {
134 m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
138 //**********************************************************************************************************************
140 int GetListCountCommand::execute(){
142 if (abort == true) { if (calledHelp) { return 0; } return 2; }
144 input = new InputData(listfile, "list");
145 list = input->getListVector();
146 string lastLabel = list->getLabel();
148 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
149 set<string> processedLabels;
150 set<string> userLabels = labels;
152 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
154 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
156 if(allLines == 1 || labels.count(list->getLabel()) == 1){
160 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
162 processedLabels.insert(list->getLabel());
163 userLabels.erase(list->getLabel());
166 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
167 string saveLabel = list->getLabel();
170 list = input->getListVector(lastLabel);
174 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());
180 //restore real lastlabel to save below
181 list->setLabel(saveLabel);
184 lastLabel = list->getLabel();
187 list = input->getListVector();
191 //output error messages about any remaining user labels
192 set<string>::iterator it;
193 bool needToRun = false;
194 for (it = userLabels.begin(); it != userLabels.end(); it++) {
195 m->mothurOut("Your file does not include the label " + *it);
196 if (processedLabels.count(lastLabel) != 1) {
197 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
200 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
204 //run last label if you need to
205 if (needToRun == true) {
206 if (list != NULL) { delete list; }
207 list = input->getListVector(lastLabel);
211 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
218 m->mothurOutEndLine();
219 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
220 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
221 m->mothurOutEndLine();
225 catch(exception& e) {
226 m->errorOut(e, "GetListCountCommand", "execute");
231 //**********************************************************************************************************************
232 //return 1 if error, 0 otherwise
233 void GetListCountCommand::process(ListVector* list) {
236 if (outputDir == "") { outputDir += m->hasPath(listfile); }
237 string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
238 m->openOutputFile(outputFileName, out);
239 outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
241 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
243 //for each bin in the list vector
244 for (int i = 0; i < list->getNumBins(); i++) {
245 if (m->control_pressed) { break; }
247 binnames = list->get(i);
250 out << i+1 << '\t' << binnames << endl;
252 vector<string> names;
253 m->splitAtComma(binnames, names);
255 for (int j = 0; j < names.size(); j++) {
256 out << names[j] << '\t' << i+1 << endl;
263 catch(exception& e) {
264 m->errorOut(e, "GetListCountCommand", "process");
268 //**********************************************************************************************************************