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; }
74 vector<string> myArray = setParameters();
76 OptionParser parser(option);
77 map<string, string> parameters = parser.getParameters();
79 ValidParameters validParameter;
80 map<string, string>::iterator it;
82 //check to make sure all parameters are valid for command
83 for (it = parameters.begin(); it != parameters.end(); it++) {
84 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
87 //initialize outputTypes
88 vector<string> tempOutNames;
89 outputTypes["otu"] = tempOutNames;
91 //if the user changes the input directory command factory will send this info to us in the output parameter
92 string inputDir = validParameter.validFile(parameters, "inputdir", false);
93 if (inputDir == "not found"){ inputDir = ""; }
96 it = parameters.find("list");
97 //user has given a template file
98 if(it != parameters.end()){
99 path = m->hasPath(it->second);
100 //if the user has not given a path then, add inputdir. else leave path alone.
101 if (path == "") { parameters["list"] = inputDir + it->second; }
105 //if the user changes the output directory command factory will send this info to us in the output parameter
106 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
108 //check for required parameters
109 listfile = validParameter.validFile(parameters, "list", true);
110 if (listfile == "not found") {
111 listfile = m->getListFile();
112 if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
113 else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
115 else if (listfile == "not open") { abort = true; }
118 //check for optional parameter and set defaults
119 // ...at some point should added some additional type checking...
120 sort = validParameter.validFile(parameters, "sort", false); if (sort == "not found") { sort = "otu"; }
121 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"; }
123 label = validParameter.validFile(parameters, "label", false);
124 if (label == "not found") { label = ""; }
126 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
127 else { allLines = 1; }
131 catch(exception& e) {
132 m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
136 //**********************************************************************************************************************
138 int GetListCountCommand::execute(){
140 if (abort == true) { if (calledHelp) { return 0; } return 2; }
142 input = new InputData(listfile, "list");
143 list = input->getListVector();
144 string lastLabel = list->getLabel();
146 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
147 set<string> processedLabels;
148 set<string> userLabels = labels;
150 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
152 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
154 if(allLines == 1 || labels.count(list->getLabel()) == 1){
158 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
160 processedLabels.insert(list->getLabel());
161 userLabels.erase(list->getLabel());
164 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
165 string saveLabel = list->getLabel();
168 list = input->getListVector(lastLabel);
172 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
175 processedLabels.insert(list->getLabel());
176 userLabels.erase(list->getLabel());
178 //restore real lastlabel to save below
179 list->setLabel(saveLabel);
182 lastLabel = list->getLabel();
185 list = input->getListVector();
189 //output error messages about any remaining user labels
190 set<string>::iterator it;
191 bool needToRun = false;
192 for (it = userLabels.begin(); it != userLabels.end(); it++) {
193 m->mothurOut("Your file does not include the label " + *it);
194 if (processedLabels.count(lastLabel) != 1) {
195 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
198 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
202 //run last label if you need to
203 if (needToRun == true) {
204 if (list != NULL) { delete list; }
205 list = input->getListVector(lastLabel);
209 if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
216 m->mothurOutEndLine();
217 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
218 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
219 m->mothurOutEndLine();
223 catch(exception& e) {
224 m->errorOut(e, "GetListCountCommand", "execute");
229 //**********************************************************************************************************************
230 //return 1 if error, 0 otherwise
231 void GetListCountCommand::process(ListVector* list) {
234 if (outputDir == "") { outputDir += m->hasPath(listfile); }
235 string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
236 m->openOutputFile(outputFileName, out);
237 outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
239 m->mothurOut(list->getLabel()); m->mothurOutEndLine();
241 //for each bin in the list vector
242 for (int i = 0; i < list->getNumBins(); i++) {
243 if (m->control_pressed) { break; }
245 binnames = list->get(i);
248 out << i+1 << '\t' << binnames << endl;
250 vector<string> names;
251 m->splitAtComma(binnames, names);
253 for (int j = 0; j < names.size(); j++) {
254 out << names[j] << '\t' << i+1 << endl;
261 catch(exception& e) {
262 m->errorOut(e, "GetListCountCommand", "process");
266 //**********************************************************************************************************************