2 * summarytaxcommand.cpp
5 * Created by westcott on 9/23/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "summarytaxcommand.h"
11 #include "phylosummary.h"
13 //**********************************************************************************************************************
14 vector<string> SummaryTaxCommand::setParameters(){
16 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptaxonomy);
17 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
18 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
19 CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(preftaxonomy);
20 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
21 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
23 vector<string> myArray;
24 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
28 m->errorOut(e, "SummaryTaxCommand", "setParameters");
32 //**********************************************************************************************************************
33 string SummaryTaxCommand::getHelpString(){
35 string helpString = "";
36 helpString += "The summary.tax command reads a taxonomy file and an optional name file, and summarizes the taxonomy information.\n";
37 helpString += "The summary.tax command parameters are taxonomy, group and name. taxonomy is required, unless you have a valid current taxonomy file.\n";
38 helpString += "The name parameter allows you to enter a name file associated with your taxonomy file. \n";
39 helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
40 helpString += "The reftaxonomy parameter allows you give the name of the reference taxonomy file used when you classified your sequences. It is not required, but providing it will keep the rankIDs in the summary file static.\n";
41 helpString += "The summary.tax command should be in the following format: \n";
42 helpString += "summary.tax(taxonomy=yourTaxonomyFile) \n";
43 helpString += "Note: No spaces between parameter labels (i.e. taxonomy), '=' and parameters (i.e.yourTaxonomyFile).\n";
47 m->errorOut(e, "SummaryTaxCommand", "getHelpString");
52 //**********************************************************************************************************************
53 SummaryTaxCommand::SummaryTaxCommand(){
55 abort = true; calledHelp = true;
57 vector<string> tempOutNames;
58 outputTypes["summary"] = tempOutNames;
61 m->errorOut(e, "SummaryTaxCommand", "SummaryTaxCommand");
65 //***************************************************************************************************************
67 SummaryTaxCommand::SummaryTaxCommand(string option) {
69 abort = false; calledHelp = false;
71 //allow user to run help
72 if(option == "help") { help(); abort = true; calledHelp = true; }
73 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
76 vector<string> myArray = setParameters();
78 OptionParser parser(option);
79 map<string,string> parameters = parser.getParameters();
81 ValidParameters validParameter;
82 map<string,string>::iterator it;
84 //check to make sure all parameters are valid for command
85 for (it = parameters.begin(); it != parameters.end(); it++) {
86 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
89 //if the user changes the input directory command factory will send this info to us in the output parameter
90 string inputDir = validParameter.validFile(parameters, "inputdir", false);
91 if (inputDir == "not found"){ inputDir = ""; }
94 it = parameters.find("taxonomy");
95 //user has given a template file
96 if(it != parameters.end()){
97 path = m->hasPath(it->second);
98 //if the user has not given a path then, add inputdir. else leave path alone.
99 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
102 it = parameters.find("name");
103 //user has given a template file
104 if(it != parameters.end()){
105 path = m->hasPath(it->second);
106 //if the user has not given a path then, add inputdir. else leave path alone.
107 if (path == "") { parameters["name"] = inputDir + it->second; }
110 it = parameters.find("group");
111 //user has given a template file
112 if(it != parameters.end()){
113 path = m->hasPath(it->second);
114 //if the user has not given a path then, add inputdir. else leave path alone.
115 if (path == "") { parameters["group"] = inputDir + it->second; }
118 it = parameters.find("reftaxonomy");
119 //user has given a template file
120 if(it != parameters.end()){
121 path = m->hasPath(it->second);
122 //if the user has not given a path then, add inputdir. else leave path alone.
123 if (path == "") { parameters["reftaxonomy"] = inputDir + it->second; }
128 //initialize outputTypes
129 vector<string> tempOutNames;
130 outputTypes["summary"] = tempOutNames;
132 //check for required parameters
133 taxfile = validParameter.validFile(parameters, "taxonomy", true);
134 if (taxfile == "not open") { abort = true; }
135 else if (taxfile == "not found") {
136 taxfile = m->getTaxonomyFile();
137 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
138 else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
139 }else { m->setTaxonomyFile(taxfile); }
141 namefile = validParameter.validFile(parameters, "name", true);
142 if (namefile == "not open") { namefile = ""; abort = true; }
143 else if (namefile == "not found") { namefile = ""; }
144 else { m->setNameFile(namefile); }
146 groupfile = validParameter.validFile(parameters, "group", true);
147 if (groupfile == "not open") { groupfile = ""; abort = true; }
148 else if (groupfile == "not found") { groupfile = ""; }
149 else { m->setGroupFile(groupfile); }
151 refTaxonomy = validParameter.validFile(parameters, "reftaxonomy", true);
152 if (refTaxonomy == "not found") { refTaxonomy = ""; m->mothurOut("reftaxonomy is not required, but if given will keep the rankIDs in the summary file static."); m->mothurOutEndLine(); }
153 else if (refTaxonomy == "not open") { refTaxonomy = ""; abort = true; }
155 //if the user changes the output directory command factory will send this info to us in the output parameter
156 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
158 outputDir += m->hasPath(taxfile); //if user entered a file with a path then preserve it
161 if (namefile == "") {
162 vector<string> files; files.push_back(taxfile);
163 parser.getNameFile(files);
168 catch(exception& e) {
169 m->errorOut(e, "SummaryTaxCommand", "SummaryTaxCommand");
173 //***************************************************************************************************************
175 int SummaryTaxCommand::execute(){
178 if (abort == true) { if (calledHelp) { return 0; } return 2; }
179 int start = time(NULL);
181 PhyloSummary* taxaSum;
182 if (refTaxonomy != "") {
183 taxaSum = new PhyloSummary(refTaxonomy, groupfile);
185 taxaSum = new PhyloSummary(groupfile);
188 if (m->control_pressed) { delete taxaSum; return 0; }
191 if (namefile == "") { numSeqs = taxaSum->summarize(taxfile); }
193 map<string, vector<string> > nameMap;
194 map<string, vector<string> >::iterator itNames;
195 m->readNames(namefile, nameMap);
197 if (m->control_pressed) { delete taxaSum; return 0; }
200 m->openInputFile(taxfile, in);
202 //read in users taxonomy file and add sequences to tree
206 in >> name >> taxon; m->gobble(in);
208 itNames = nameMap.find(name);
210 if (itNames == nameMap.end()) {
211 m->mothurOut("[ERROR]: " + name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
213 for (int i = 0; i < itNames->second.size(); i++) {
215 taxaSum->addSeqToTree(itNames->second[i], taxon); //add it as many times as there are identical seqs
217 itNames->second.clear();
218 nameMap.erase(itNames->first);
224 if (m->control_pressed) { delete taxaSum; return 0; }
228 string summaryFile = outputDir + m->getRootName(m->getSimpleName(taxfile)) + "tax.summary";
229 m->openOutputFile(summaryFile, outTaxTree);
230 taxaSum->print(outTaxTree);
235 if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
237 m->mothurOutEndLine();
238 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
239 m->mothurOutEndLine();
240 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
241 m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
242 m->mothurOutEndLine();
246 catch(exception& e) {
247 m->errorOut(e, "SummaryTaxCommand", "execute");
251 /**************************************************************************************/