5 * Created by westcott on 11/20/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
10 #include "phylotypecommand.h"
11 #include "phylotree.h"
12 #include "listvector.hpp"
13 #include "rabundvector.hpp"
14 #include "sabundvector.hpp"
16 //**********************************************************************************************************************
17 vector<string> PhylotypeCommand::setParameters(){
19 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);
20 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
21 CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
22 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
23 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
24 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
26 vector<string> myArray;
27 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
31 m->errorOut(e, "PhylotypeCommand", "setParameters");
35 //**********************************************************************************************************************
36 string PhylotypeCommand::getHelpString(){
38 string helpString = "";
39 helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n";
40 helpString += "The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n";
41 helpString += "The cutoff parameter allows you to specify the level you want to stop at. The default is the highest level in your taxonomy file. \n";
42 helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
43 helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";
44 helpString += "The label parameter allows you to specify which level you would like, and are separated by dashes. The default all levels in your taxonomy file. \n";
45 helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
46 helpString += "The phylotype command should be in the following format: \n";
47 helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
48 helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
52 m->errorOut(e, "PhylotypeCommand", "getHelpString");
56 //**********************************************************************************************************************
57 string PhylotypeCommand::getOutputPattern(string type) {
61 if (type == "list") { pattern = "[filename],[tag],list"; }
62 else if (type == "rabund") { pattern = "[filename],[tag],rabund"; }
63 else if (type == "sabund") { pattern = "[filename],[tag],sabund"; }
64 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
69 m->errorOut(e, "PhylotypeCommand", "getOutputPattern");
73 //**********************************************************************************************************************
74 PhylotypeCommand::PhylotypeCommand(){
76 abort = true; calledHelp = true;
78 vector<string> tempOutNames;
79 outputTypes["list"] = tempOutNames;
80 outputTypes["sabund"] = tempOutNames;
81 outputTypes["rabund"] = tempOutNames;
84 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
88 /**********************************************************************************************************************/
89 PhylotypeCommand::PhylotypeCommand(string option) {
91 abort = false; calledHelp = false;
93 //allow user to run help
94 if(option == "help") { help(); abort = true; calledHelp = true; }
95 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
98 vector<string> myArray = setParameters();
100 OptionParser parser(option);
101 map<string, string> parameters = parser.getParameters();
103 ValidParameters validParameter;
104 map<string, string>::iterator it;
106 //check to make sure all parameters are valid for command
107 for (it = parameters.begin(); it != parameters.end(); it++) {
108 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
111 //initialize outputTypes
112 vector<string> tempOutNames;
113 outputTypes["list"] = tempOutNames;
114 outputTypes["sabund"] = tempOutNames;
115 outputTypes["rabund"] = tempOutNames;
117 //if the user changes the input directory command factory will send this info to us in the output parameter
118 string inputDir = validParameter.validFile(parameters, "inputdir", false);
119 if (inputDir == "not found"){ inputDir = ""; }
122 it = parameters.find("taxonomy");
123 //user has given a template file
124 if(it != parameters.end()){
125 path = m->hasPath(it->second);
126 //if the user has not given a path then, add inputdir. else leave path alone.
127 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
130 it = parameters.find("name");
131 //user has given a template file
132 if(it != parameters.end()){
133 path = m->hasPath(it->second);
134 //if the user has not given a path then, add inputdir. else leave path alone.
135 if (path == "") { parameters["name"] = inputDir + it->second; }
139 taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
140 if (taxonomyFileName == "not found") {
141 taxonomyFileName = m->getTaxonomyFile();
142 if (taxonomyFileName != "") { m->mothurOut("Using " + taxonomyFileName + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
144 m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine();
147 }else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; }
148 else { m->setTaxonomyFile(taxonomyFileName); }
150 namefile = validParameter.validFile(parameters, "name", true);
151 if (namefile == "not open") { namefile = ""; abort = true; }
152 else if (namefile == "not found") { namefile = ""; }
153 else { readNamesFile(); m->setNameFile(namefile); }
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(taxonomyFileName); //if user entered a file with a path then preserve it
161 string temp = validParameter.validFile(parameters, "cutoff", false);
162 if (temp == "not found") { temp = "-1"; }
163 m->mothurConvert(temp, cutoff);
165 label = validParameter.validFile(parameters, "label", false);
166 if (label == "not found") { label = ""; allLines = 1; }
168 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
169 else { allLines = 1; }
172 if (namefile == "") {
173 vector<string> files; files.push_back(taxonomyFileName);
174 parser.getNameFile(files);
179 catch(exception& e) {
180 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
184 /**********************************************************************************************************************/
186 int PhylotypeCommand::execute(){
189 if (abort == true) { if (calledHelp) { return 0; } return 2; }
191 //reads in taxonomy file and makes all the taxonomies the same length
192 //by appending the last taxon to a given taxonomy as many times as needed to
193 //make it as long as the longest taxonomy in the file
194 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputDir);
196 if (m->control_pressed) { delete taxEqual; return 0; }
198 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
202 //build taxonomy tree from equalized file
203 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
204 vector<int> leaves = tree->getGenusNodes();
206 //store leaf nodes in current map
207 for (int i = 0; i < leaves.size(); i++) { currentNodes[leaves[i]] = leaves[i]; }
210 if (tree->get(leaves[0]).parent == -1) { m->mothurOut("Empty Tree"); m->mothurOutEndLine(); done = true; }
212 if (m->control_pressed) { delete tree; return 0; }
214 string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
215 map<string, string> variables;
216 variables["[filename]"] = fileroot;
217 variables["[tag]"] = "tx";
219 string outputListFile = getOutputFileName("list",variables);
220 m->openOutputFile(outputListFile, outList);
222 string outputSabundFile = getOutputFileName("sabund",variables);
223 m->openOutputFile(outputSabundFile, outSabund);
225 string outputRabundFile = getOutputFileName("rabund",variables);
226 m->openOutputFile(outputRabundFile, outRabund);
228 outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
229 outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
230 outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
233 //start at leaves of tree and work towards root, processing the labels the user wants
234 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
236 string level = toString(count);
239 if (m->control_pressed) {
240 outRabund.close(); outSabund.close(); outList.close();
241 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
242 delete tree; return 0;
245 //is this a level the user want output for
246 if(allLines == 1 || labels.count(level) == 1){
249 m->mothurOut(level); m->mothurOutEndLine();
252 list.setLabel(level);
254 //go through nodes and build listvector
255 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
258 TaxNode node = tree->get(itCurrent->first);
259 parentNodes[node.parent] = node.parent;
261 vector<string> names = node.accessions;
263 //make the names compatable with listvector
265 for (int i = 0; i < names.size(); i++) {
267 if (names[i] != "unknown") {
268 if (namefile != "") {
269 map<string, string>::iterator itNames = namemap.find(names[i]); //make sure this name is in namefile
271 if (itNames != namemap.end()) { name += namemap[names[i]] + ","; } //you found it in namefile
272 else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
274 }else{ name += names[i] + ","; }
278 if (m->control_pressed) { break; }
280 name = name.substr(0, name.length()-1); //rip off extra ','
281 //add bin to list vector
282 if (name != "") { list.push_back(name); } //caused by unknown
288 list.getRAbundVector().print(outRabund);
290 list.getSAbundVector().print(outSabund);
297 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
298 int parent = tree->get(itCurrent->first).parent;
299 parentNodes[parent] = parent;
304 currentNodes = parentNodes;
307 //have we reached the rootnode
308 if (tree->get(currentNodes.begin()->first).parent == -1) { done = true; }
317 if (m->control_pressed) {
318 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
322 //set list file as new current listfile
324 itTypes = outputTypes.find("list");
325 if (itTypes != outputTypes.end()) {
326 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
329 //set rabund file as new current rabundfile
330 itTypes = outputTypes.find("rabund");
331 if (itTypes != outputTypes.end()) {
332 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
335 //set sabund file as new current sabundfile
336 itTypes = outputTypes.find("sabund");
337 if (itTypes != outputTypes.end()) {
338 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
341 m->mothurOutEndLine();
342 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
343 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
344 m->mothurOutEndLine();
349 catch(exception& e) {
350 m->errorOut(e, "PhylotypeCommand", "execute");
354 /*****************************************************************/
355 int PhylotypeCommand::readNamesFile() {
359 m->openInputFile(namefile, in);
361 string first, second;
362 map<string, string>::iterator itNames;
365 in >> first >> second; m->gobble(in);
367 itNames = namemap.find(first);
368 if (itNames == namemap.end()) {
369 namemap[first] = second;
370 }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
376 catch(exception& e) {
377 m->errorOut(e, "PhylotypeCommand", "readNamesFile");
382 /**********************************************************************************************************************/