2 * otuhierarchycommand.cpp
5 * Created by westcott on 1/19/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "otuhierarchycommand.h"
12 //**********************************************************************************************************************
13 vector<string> OtuHierarchyCommand::setParameters(){
15 CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput);
16 CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
17 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
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, "OtuHierarchyCommand", "setParameters");
30 //**********************************************************************************************************************
31 string OtuHierarchyCommand::getHelpString(){
33 string helpString = "";
34 helpString += "The otu.hierarchy command is used to see how otus relate at two distances. \n";
35 helpString += "The otu.hierarchy command parameters are list, label and output. list and label parameters are required. \n";
36 helpString += "The output parameter allows you to output the names of the sequence in the OTUs or the OTU numbers. Options are name and number, default is name. \n";
37 helpString += "The otu.hierarchy command should be in the following format: \n";
38 helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n";
39 helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n";
40 helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n";
41 helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
45 m->errorOut(e, "OtuHierarchyCommand", "getHelpString");
50 //**********************************************************************************************************************
51 OtuHierarchyCommand::OtuHierarchyCommand(){
53 abort = true; calledHelp = true;
55 vector<string> tempOutNames;
56 outputTypes["otuheirarchy"] = tempOutNames;
59 m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
63 //**********************************************************************************************************************
64 OtuHierarchyCommand::OtuHierarchyCommand(string option) {
66 abort = false; calledHelp = false;
68 //allow user to run help
69 if(option == "help") { help(); abort = true; calledHelp = true; }
70 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
73 vector<string> myArray = setParameters();
75 OptionParser parser(option);
76 map<string,string> parameters = parser.getParameters();
78 ValidParameters validParameter;
79 map<string,string>::iterator it;
81 //check to make sure all parameters are valid for command
82 for (it = parameters.begin(); it != parameters.end(); it++) {
83 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
86 //initialize outputTypes
87 vector<string> tempOutNames;
88 outputTypes["otuheirarchy"] = tempOutNames;
90 //if the user changes the input directory command factory will send this info to us in the output parameter
91 string inputDir = validParameter.validFile(parameters, "inputdir", false);
92 if (inputDir == "not found"){ inputDir = ""; }
95 it = parameters.find("list");
96 //user has given a template file
97 if(it != parameters.end()){
98 path = m->hasPath(it->second);
99 //if the user has not given a path then, add inputdir. else leave path alone.
100 if (path == "") { parameters["list"] = inputDir + it->second; }
104 listFile = validParameter.validFile(parameters, "list", true);
105 if (listFile == "not found") {
106 listFile = m->getListFile();
107 if (listFile != "") { m->mothurOut("Using " + listFile + " as input file for the list parameter."); m->mothurOutEndLine(); }
109 m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
112 }else if (listFile == "not open") { abort = true; }
113 else { m->setListFile(listFile); }
115 //if the user changes the output directory command factory will send this info to us in the output parameter
116 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
118 outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
121 //check for optional parameter and set defaults
122 // ...at some point should added some additional type checking...
123 label = validParameter.validFile(parameters, "label", false);
124 if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
126 m->splitAtDash(label, labels);
127 if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
130 output = validParameter.validFile(parameters, "output", false); if (output == "not found") { output = "name"; }
132 if ((output != "name") && (output != "number")) { m->mothurOut("output options are name and number. I will use name."); m->mothurOutEndLine(); output = "name"; }
136 catch(exception& e) {
137 m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand");
141 //**********************************************************************************************************************
143 int OtuHierarchyCommand::execute(){
146 if (abort == true) { if (calledHelp) { return 0; } return 2; }
148 //get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector)
149 vector<ListVector> lists = getListVectors();
151 if (m->control_pressed) { outputTypes.clear(); return 0; }
153 //determine which is little and which is big, putting little first
154 if (lists.size() == 2) {
155 //if big is first swap them
156 if (lists[0].getNumBins() < lists[1].getNumBins()) {
157 reverse(lists.begin(), lists.end());
160 m->mothurOut("error getting listvectors, unable to read 2 different vectors, check your label inputs."); m->mothurOutEndLine(); return 0;
163 //map sequences to bin number in the "little" otu
164 map<string, int> littleBins;
165 for (int i = 0; i < lists[0].getNumBins(); i++) {
167 if (m->control_pressed) { return 0; }
169 string names = lists[0].get(i);
172 while (names.find_first_of(',') != -1) {
173 string name = names.substr(0,names.find_first_of(','));
174 names = names.substr(names.find_first_of(',')+1, names.length());
175 littleBins[name] = i;
179 littleBins[names] = i;
183 string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
184 m->openOutputFile(outputFileName, out);
186 //go through each bin in "big" otu and output the bins in "little" otu which created it
187 for (int i = 0; i < lists[1].getNumBins(); i++) {
189 if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
191 string names = lists[1].get(i);
194 if (output == "name") { out << names << '\t'; }
195 else { out << i << '\t'; }
197 map<int, int> bins; //bin numbers in little that are in this bin in big
198 map<int, int>::iterator it;
201 while (names.find_first_of(',') != -1) {
202 string name = names.substr(0,names.find_first_of(','));
203 names = names.substr(names.find_first_of(',')+1, names.length());
204 bins[littleBins[name]] = littleBins[name];
208 bins[littleBins[names]] = littleBins[names];
211 for (it = bins.begin(); it != bins.end(); it++) {
212 if (output == "name") { col2 += lists[0].get(it->first) + "\t"; }
213 else { col2 += toString(it->first) + "\t"; }
222 if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
224 m->mothurOutEndLine();
225 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
226 m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName);
227 m->mothurOutEndLine();
231 catch(exception& e) {
232 m->errorOut(e, "OtuHierarchyCommand", "execute");
237 //**********************************************************************************************************************
238 //returns a vector of listVectors where "little" vector is first
239 vector<ListVector> OtuHierarchyCommand::getListVectors() {
242 int pos; //to use in smart distancing, position of last read in file
244 vector<ListVector> lists;
246 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
247 set<string> processedLabels;
248 set<string> userLabels = labels;
252 m->openInputFile(listFile, in);
254 //get first list vector in file
255 ListVector* list = NULL;
256 string lastLabel = "";
260 list = new ListVector(in);
262 lastLabel = list->getLabel();
265 while ((list != NULL) && (userLabels.size() != 0)) {
267 if (m->control_pressed) { in.close(); delete list; return lists; }
269 //is this a listvector that we want?
270 if(labels.count(list->getLabel()) == 1){
272 //make copy of listvector
273 ListVector temp(*list);
274 lists.push_back(temp);
276 processedLabels.insert(list->getLabel());
277 userLabels.erase(list->getLabel());
280 //you have a label the user want that is smaller than this label and the last label has not already been processed
281 if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
282 string saveLabel = list->getLabel();
283 int savePos = in.tellg();
285 //get smart distance line
289 list = new ListVector(in);
290 }else { list = NULL; }
292 //make copy of listvector
293 ListVector temp(*list);
294 lists.push_back(temp);
296 processedLabels.insert(list->getLabel());
297 userLabels.erase(list->getLabel());
299 //restore real lastlabel to save below
300 list->setLabel(saveLabel);
304 lastLabel = list->getLabel();
311 list = new ListVector(in);
313 }else { list = NULL; }
316 if (m->control_pressed) { in.close(); return lists; }
318 //output error messages about any remaining user labels
319 set<string>::iterator it;
320 bool needToRun = false;
321 for (it = userLabels.begin(); it != userLabels.end(); it++) {
322 m->mothurOut("Your file does not include the label " + *it);
323 if (processedLabels.count(lastLabel) != 1) {
324 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
327 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
331 if (m->control_pressed) { in.close(); return lists; }
333 //run last label if you need to
334 if (needToRun == true) {
335 if (list != NULL) { delete list; }
339 list = new ListVector(in);
341 //make copy of listvector
342 ListVector temp(*list);
343 lists.push_back(temp);
352 catch(exception& e) {
353 m->errorOut(e, "OtuHierarchyCommand", "getListVectors");
358 //**********************************************************************************************************************