2 // GetCoreMicroBiomeCommand.cpp
5 // Created by John Westcott on 5/8/12.
6 // Copyright (c) 2012 Schloss Lab. All rights reserved.
9 #include "getcoremicrobiomecommand.h"
12 //**********************************************************************************************************************
13 vector<string> GetCoreMicroBiomeCommand::setParameters(){
15 CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(pshared);
16 CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(prelabund);
17 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
18 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
19 CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "","",false,false); parameters.push_back(poutput);
20 CommandParameter pabund("abundance", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pabund);
21 CommandParameter psamples("samples", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(psamples);
22 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
23 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
25 vector<string> myArray;
26 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
30 m->errorOut(e, "GetCoreMicroBiomeCommand", "setParameters");
34 //**********************************************************************************************************************
35 string GetCoreMicroBiomeCommand::getHelpString(){
37 string helpString = "";
38 helpString += "The get.coremicrobiome determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.\n";
39 helpString += "The get.coremicrobiome parameters are: shared, relabund, groups, label, output, abundance and samples. Shared or relabund is required.\n";
40 helpString += "The label parameter is used to analyze specific labels in your input.\n";
41 helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n";
42 helpString += "The output parameter is used to specify whether you would like the fraction of OTU's or OTU count outputted. Options are fraction or count. Default=fraction.\n";
43 helpString += "The abundance parameter allows you to specify an abundance you would like the OTU names outputted for. Must be an integer between 0 and 100, indicating the relative abundance. \n";
44 helpString += "The samples parameter allows you to specify the minimum number of samples you would like the OTU names outputted for. Must be an interger between 1 and number of samples in your file.\n";
45 helpString += "The new command should be in the following format: get.coremicrobiome(shared=yourSharedFile)\n";
46 helpString += "get.coremicrobiom(shared=final.an.shared, abund=30)\n";
50 m->errorOut(e, "GetCoreMicroBiomeCommand", "getHelpString");
54 //**********************************************************************************************************************
55 string GetCoreMicroBiomeCommand::getOutputPattern(string type) {
59 if (type == "coremicrobiome") { pattern = "[filename],[tag],core.microbiome"; }
60 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
65 m->errorOut(e, "GetCoreMicroBiomeCommand", "getOutputPattern");
69 //**********************************************************************************************************************
70 GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){
72 abort = true; calledHelp = true;
74 vector<string> tempOutNames;
75 outputTypes["coremicrobiome"] = tempOutNames;
78 m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
82 //**********************************************************************************************************************
83 GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(string option) {
85 abort = false; calledHelp = false; allLines = 1;
87 //allow user to run help
88 if(option == "help") { help(); abort = true; calledHelp = true; }
89 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
92 //valid paramters for this command
93 vector<string> myArray = setParameters();
95 OptionParser parser(option);
96 map<string,string> parameters = parser.getParameters();
98 ValidParameters validParameter;
99 map<string,string>::iterator it;
100 //check to make sure all parameters are valid for command
101 for (it = parameters.begin(); it != parameters.end(); it++) {
102 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
106 //if the user changes the input directory command factory will send this info to us in the output parameter
107 string inputDir = validParameter.validFile(parameters, "inputdir", false);
108 if (inputDir == "not found"){ inputDir = ""; }
112 it = parameters.find("relabund");
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["relabund"] = inputDir + it->second; }
120 it = parameters.find("shared");
121 //user has given a template file
122 if(it != parameters.end()){
123 path = m->hasPath(it->second);
124 //if the user has not given a path then, add inputdir. else leave path alone.
125 if (path == "") { parameters["shared"] = inputDir + it->second; }
129 vector<string> tempOutNames;
130 outputTypes["coremicrobiome"] = tempOutNames;
132 //check for parameters
133 sharedfile = validParameter.validFile(parameters, "shared", true);
134 if (sharedfile == "not open") { abort = true; }
135 else if (sharedfile == "not found") { sharedfile = ""; }
136 else { inputFileName = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
138 relabundfile = validParameter.validFile(parameters, "relabund", true);
139 if (relabundfile == "not open") { abort = true; }
140 else if (relabundfile == "not found") { relabundfile = ""; }
141 else { inputFileName = relabundfile; format = "relabund"; m->setRelAbundFile(relabundfile); }
143 if ((relabundfile == "") && (sharedfile == "")) {
144 //is there are current file available for either of these?
145 //give priority to shared, then relabund
146 sharedfile = m->getSharedFile();
147 if (sharedfile != "") { inputFileName = sharedfile; format="sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
149 relabundfile = m->getRelAbundFile();
150 if (relabundfile != "") { inputFileName = relabundfile; format="relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
152 m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
158 //if the user changes the output directory command factory will send this info to us in the output parameter
159 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
160 outputDir = m->hasPath(inputFileName); //if user entered a file with a path then preserve it
163 string groups = validParameter.validFile(parameters, "groups", false);
164 if (groups == "not found") { groups = ""; }
165 else { m->splitAtDash(groups, Groups); }
166 m->setGroups(Groups);
168 string label = validParameter.validFile(parameters, "label", false);
169 if (label == "not found") { label = ""; }
171 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
172 else { allLines = 1; }
175 output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "fraction"; }
177 if ((output != "fraction") && (output != "count")) { m->mothurOut(output + " is not a valid output form. Options are fraction and count. I will use fraction."); m->mothurOutEndLine(); output = "fraction"; }
179 string temp = validParameter.validFile(parameters, "abundance", false); if (temp == "not found"){ temp = "-1"; }
180 m->mothurConvert(temp, abund);
183 if ((abund < 0) || (abund > 100)) { m->mothurOut(toString(abund) + " is not a valid number for abund. Must be an integer between 0 and 100.\n"); }
186 temp = validParameter.validFile(parameters, "samples", false); if (temp == "not found"){ temp = "-1"; }
187 m->mothurConvert(temp, samples);
192 catch(exception& e) {
193 m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
197 //**********************************************************************************************************************
199 int GetCoreMicroBiomeCommand::execute(){
202 if (abort == true) { if (calledHelp) { return 0; } return 2; }
204 InputData input(inputFileName, format);
205 vector<SharedRAbundFloatVector*> lookup = input.getSharedRAbundFloatVectors();
206 string lastLabel = lookup[0]->getLabel();
209 if ((samples < 1) || (samples > lookup.size())) { m->mothurOut(toString(samples) + " is not a valid number for samples. Must be an integer between 1 and the number of samples in your file. Your file contains " + toString(lookup.size()) + " samples, so I will use that.\n"); samples = lookup.size(); }
213 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
214 set<string> processedLabels;
215 set<string> userLabels = labels;
217 //as long as you are not at the end of the file or done wih the lines you want
218 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
220 if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
222 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
224 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
228 processedLabels.insert(lookup[0]->getLabel());
229 userLabels.erase(lookup[0]->getLabel());
232 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
233 string saveLabel = lookup[0]->getLabel();
235 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
236 lookup = input.getSharedRAbundFloatVectors(lastLabel);
237 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
241 processedLabels.insert(lookup[0]->getLabel());
242 userLabels.erase(lookup[0]->getLabel());
244 //restore real lastlabel to save below
245 lookup[0]->setLabel(saveLabel);
248 lastLabel = lookup[0]->getLabel();
249 //prevent memory leak
250 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
252 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
254 //get next line to process
255 lookup = input.getSharedRAbundFloatVectors();
258 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
260 //output error messages about any remaining user labels
261 set<string>::iterator it;
262 bool needToRun = false;
263 for (it = userLabels.begin(); it != userLabels.end(); it++) {
264 m->mothurOut("Your file does not include the label " + *it);
265 if (processedLabels.count(lastLabel) != 1) {
266 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
269 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
273 //run last label if you need to
274 if (needToRun == true) {
275 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
276 lookup = input.getSharedRAbundFloatVectors(lastLabel);
278 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
282 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
285 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
287 //output files created by command
288 m->mothurOutEndLine();
289 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
290 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
291 m->mothurOutEndLine();
295 catch(exception& e) {
296 m->errorOut(e, "GetCoreMicroBiomeCommand", "execute");
300 //**********************************************************************************************************************
302 int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
304 map<string, string> variables;
305 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
306 variables["[tag]"] = lookup[0]->getLabel();
307 string outputFileName = getOutputFileName("coremicrobiome", variables);
308 outputNames.push_back(outputFileName); outputTypes["coremicrobiome"].push_back(outputFileName);
310 m->openOutputFile(outputFileName, out);
312 int numSamples = lookup.size();
313 int numOtus = lookup[0]->getNumBins();
315 //table is 100 by numsamples
316 //question we are answering is: what fraction of OTUs in a study have a relative abundance at or above %X
317 //in at least %Y samples. x goes from 0 to 100, y from 1 to numSamples
318 vector< vector<double> > table; table.resize(101);
319 for (int i = 0; i < table.size(); i++) { table[i].resize(numSamples, 0.0); }
321 map<int, vector<string> > otuNames;
322 if ((abund != -1) && (samples == -1)) { //fill with all samples
323 for (int i = 0; i < numSamples; i++) {
325 otuNames[i+1] = temp;
327 }else if ((abund == -1) && (samples != -1)) { //fill with all relabund
328 for (int i = 0; i < 101; i++) {
332 }else if ((abund != -1) && (samples != -1)) { //only one line is wanted
334 otuNames[abund] = temp;
337 for (int i = 0; i < numOtus; i++) {
339 if (m->control_pressed) { break; }
341 //count number of samples in this otu with a relabund >= spot in count
342 vector<int> counts; counts.resize(101, 0);
344 for (int j = 0; j < lookup.size(); j++) {
345 double relabund = lookup[j]->getAbundance(i);
346 int wholeRelabund = (int) (floor(relabund*100));
347 for (int k = 0; k < wholeRelabund+1; k++) { counts[k]++; }
350 //add this otus info to table
351 for (int j = 0; j < table.size(); j++) {
352 for (int k = 0; k < counts[j]; k++) { table[j][k]++; }
354 if ((abund == -1) && (samples != -1)) { //we want all OTUs with this number of samples
355 if (counts[j] >= samples) { otuNames[j].push_back(m->currentBinLabels[i]); }
356 }else if ((abund != -1) && (samples == -1)) { //we want all OTUs with this relabund
358 for (int k = 0; k < counts[j]; k++) { otuNames[k+1].push_back(m->currentBinLabels[i]); }
360 }else if ((abund != -1) && (samples != -1)) { //we want only OTUs with this relabund for this number of samples
361 if ((j == abund) && (counts[j] >= samples)) {
362 otuNames[j].push_back(m->currentBinLabels[i]);
369 if (output == "fraction") { out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); }
370 out << "NumSamples\t";
372 //convert table counts to percents
373 for (int i = 0; i < table.size(); i++) {
374 out << "Relabund-" << i << "%\t";
375 if (m->control_pressed) { break; }
376 for (int j = 0; j < table[i].size(); j++) { if (output == "fraction") { table[i][j] /= (double) numOtus; } }
380 for (int i = 0; i < numSamples; i++) {
381 if (m->control_pressed) { break; }
383 for (int j = 0; j < table.size(); j++) { out << table[j][i] << '\t'; }
389 if (m->control_pressed) { return 0; }
391 if ((samples != -1) || (abund != -1)) {
392 string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomelist";
393 outputNames.push_back(outputFileName2); outputTypes["coremicrobiome"].push_back(outputFileName2);
395 m->openOutputFile(outputFileName2, out2);
397 if ((abund == -1) && (samples != -1)) { //we want all OTUs with this number of samples
398 out2 << "Relabund%\tOTUList_for_samples=" << samples << "\n";
399 }else if ((abund != -1) && (samples == -1)) { //we want all OTUs with this relabund
400 out2 << "Samples\tOTUList_for_abund=" << abund << "\n";
401 }else if ((abund != -1) && (samples != -1)) { //we want only OTUs with this relabund for this number of samples
402 out2 << "Relabund%\tOTUList_for_samples=" << samples << "\n";
405 for (map<int, vector<string> >::iterator it = otuNames.begin(); it != otuNames.end(); it++) {
406 if (m->control_pressed) { break; }
408 vector<string> temp = it->second;
409 string list = m->makeList(temp);
411 out2 << it->first << '\t' << list << endl;
419 catch(exception& e) {
420 m->errorOut(e, "GetCoreMicroBiomeCommand", "createTable");
425 //**********************************************************************************************************************