5 * Created by westcott on 5/11/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "clearcutcommand.h"
19 //**********************************************************************************************************************
20 vector<string> ClearcutCommand::setParameters(){
22 CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pphylip);
23 CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pfasta);
24 CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pverbose);
25 CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pquiet);
26 CommandParameter pversion("version", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pversion);
27 CommandParameter pseed("seed", "String", "", "", "*", "", "",false,false); parameters.push_back(pseed);
28 CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnorandom);
29 CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshuffle);
30 CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pneighbor);
31 CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpblen);
32 CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpdist);
33 CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pDNA);
34 CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pprotein);
35 CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pjukes);
36 CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkimura);
37 CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pstdout);
38 CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "",false,false); parameters.push_back(pntrees);
39 CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "",false,false); parameters.push_back(pmatrixout);
40 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
41 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
43 vector<string> myArray;
44 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
48 m->errorOut(e, "ClearcutCommand", "setParameters");
52 //**********************************************************************************************************************
53 string ClearcutCommand::getHelpString(){
55 string helpString = "";
56 helpString += "The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n";
57 helpString += "For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n";
58 helpString += "The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n";
59 helpString += "The phylip parameter allows you to enter your phylip formatted distance matrix. \n";
60 helpString += "The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n";
62 helpString += "The version parameter prints out the version of clearcut you are using, default=F. \n";
63 helpString += "The verbose parameter prints out more output from clearcut, default=F. \n";
64 helpString += "The quiet parameter turns on silent operation mode, default=F. \n";
65 helpString += "The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n";
66 helpString += "The norandom parameter allows you to attempt joins deterministically, default=F. \n";
67 helpString += "The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n";
68 helpString += "The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=T. \n";
70 helpString += "The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n";
71 helpString += "The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n";
73 helpString += "The stdout parameter outputs your tree to STDOUT, default=F. \n";
74 helpString += "The matrixout parameter allows you to specify a filename to output a distance matrix to. \n";
75 helpString += "The ntrees parameter allows you to specify the number of output trees, default=1. \n";
76 helpString += "The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n";
77 helpString += "The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n";
79 helpString += "The clearcut command should be in the following format: \n";
80 helpString += "clearcut(phylip=yourDistanceFile) \n";
81 helpString += "Example: clearcut(phylip=abrecovery.phylip.dist) \n";
85 m->errorOut(e, "ClearcutCommand", "getHelpString");
90 //**********************************************************************************************************************
91 ClearcutCommand::ClearcutCommand(){
93 abort = true; calledHelp = true;
95 vector<string> tempOutNames;
96 outputTypes["tree"] = tempOutNames;
97 outputTypes["matrixout"] = tempOutNames;
100 m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
104 /**************************************************************************************/
105 ClearcutCommand::ClearcutCommand(string option) {
107 abort = false; calledHelp = false;
109 //allow user to run help
110 if(option == "help") { help(); abort = true; calledHelp = true; }
111 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
114 vector<string> myArray = setParameters();
116 OptionParser parser(option);
117 map<string,string> parameters = parser.getParameters();
119 ValidParameters validParameter;
120 map<string, string>::iterator it;
122 //check to make sure all parameters are valid for command
123 for (it = parameters.begin(); it != parameters.end(); it++) {
124 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
127 //initialize outputTypes
128 vector<string> tempOutNames;
129 outputTypes["tree"] = tempOutNames;
130 outputTypes["matrixout"] = tempOutNames;
132 //if the user changes the input directory command factory will send this info to us in the output parameter
133 string inputDir = validParameter.validFile(parameters, "inputdir", false);
134 if (inputDir == "not found"){ inputDir = ""; }
137 it = parameters.find("fasta");
138 //user has given a template file
139 if(it != parameters.end()){
140 path = m->hasPath(it->second);
141 //if the user has not given a path then, add inputdir. else leave path alone.
142 if (path == "") { parameters["fasta"] = inputDir + it->second; }
145 it = parameters.find("phylip");
146 //user has given a template file
147 if(it != parameters.end()){
148 path = m->hasPath(it->second);
149 //if the user has not given a path then, add inputdir. else leave path alone.
150 if (path == "") { parameters["phylip"] = inputDir + it->second; }
154 //check for required parameters
155 fastafile = validParameter.validFile(parameters, "fasta", true);
156 if (fastafile == "not open") { fastafile = ""; abort = true; }
157 else if (fastafile == "not found") { fastafile = ""; }
158 else { inputFile = fastafile; m->setFastaFile(fastafile); }
160 phylipfile = validParameter.validFile(parameters, "phylip", true);
161 if (phylipfile == "not open") { phylipfile = ""; abort = true; }
162 else if (phylipfile == "not found") { phylipfile = ""; }
163 else { inputFile = phylipfile; m->setPhylipFile(phylipfile); }
165 if ((phylipfile == "") && (fastafile == "")) {
166 //is there are current file available for either of these?
167 //give priority to phylip, then fasta
168 phylipfile = m->getPhylipFile();
169 if (phylipfile != "") { inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
171 fastafile = m->getFastaFile();
172 if (fastafile != "") { inputFile = fastafile; m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
174 m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine();
179 if ((phylipfile != "") && (fastafile != "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file, not BOTH."); m->mothurOutEndLine(); abort=true; }
182 //if the user changes the output directory command factory will send this info to us in the output parameter
183 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputFile); }
186 temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }
187 version = m->isTrue(temp);
189 temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }
190 verbose = m->isTrue(temp);
192 temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }
193 quiet = m->isTrue(temp);
195 seed = validParameter.validFile(parameters, "seed", false); if (seed == "not found"){ seed = "*"; }
197 temp = validParameter.validFile(parameters, "norandom", false); if (temp == "not found"){ temp = "F"; }
198 norandom = m->isTrue(temp);
200 temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }
201 shuffle = m->isTrue(temp);
203 temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "T"; }
204 neighbor = m->isTrue(temp);
206 temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }
207 DNA = m->isTrue(temp);
209 temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }
210 protein = m->isTrue(temp);
212 temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }
213 jukes = m->isTrue(temp);
215 temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }
216 kimura = m->isTrue(temp);
218 temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }
219 stdoutWanted = m->isTrue(temp);
221 matrixout = validParameter.validFile(parameters, "matrixout", false); if (matrixout == "not found"){ matrixout = ""; }
223 ntrees = validParameter.validFile(parameters, "ntrees", false); if (ntrees == "not found"){ ntrees = "1"; }
225 temp = validParameter.validFile(parameters, "expblen", false); if (temp == "not found"){ temp = "F"; }
226 expblen = m->isTrue(temp);
228 temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }
229 expdist = m->isTrue(temp);
231 if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }
235 catch(exception& e) {
236 m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
240 /**************************************************************************************/
241 int ClearcutCommand::execute() {
244 if (abort == true) { if (calledHelp) { return 0; } return 2; }
247 string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
248 outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
252 char* tempClearcut = new char[8];
253 strcpy(tempClearcut, "clearcut");
254 cPara.push_back(tempClearcut);
256 //you gave us a distance matrix
257 if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); }
259 //you gave us a fastafile
260 if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); }
262 if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); }
263 if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); }
264 if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); }
266 string tempSeed = "--seed=" + seed;
267 char* temp = new char[tempSeed.length()];
268 strcpy(temp, tempSeed.c_str());
269 cPara.push_back(temp);
271 if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); }
272 if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); }
273 if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); }
275 string tempIn = "--in=" + inputFile;
276 char* tempI = new char[tempIn.length()];
277 strcpy(tempI, tempIn.c_str());
278 cPara.push_back(tempI);
280 if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); }
282 string tempOut = "--out=" + outputName;
284 char* temp = new char[tempOut.length()];
285 strcpy(temp, tempOut.c_str());
286 cPara.push_back(temp);
289 if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); }
290 if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); }
291 if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); }
292 if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); }
293 if (matrixout != "") {
294 string tempMatrix = "--matrixout=" + outputDir + matrixout;
295 char* temp = new char[tempMatrix.length()];
296 strcpy(temp, tempMatrix.c_str());
297 cPara.push_back(temp);
298 outputNames.push_back((outputDir + matrixout));
299 outputTypes["matrixout"].push_back((outputDir + matrixout));
303 string tempNtrees = "--ntrees=" + ntrees;
304 char* temp = new char[tempNtrees.length()];
305 strcpy(temp, tempNtrees.c_str());
306 cPara.push_back(temp);
309 if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); }
310 if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); }
312 char** clearcutParameters;
313 clearcutParameters = new char*[cPara.size()];
314 for (int i = 0; i < cPara.size(); i++) { clearcutParameters[i] = cPara[i]; }
315 int numArgs = cPara.size();
317 clearcut_main(numArgs, clearcutParameters);
320 for(int i = 0; i < cPara.size(); i++) { delete[] cPara[i]; }
321 delete[] clearcutParameters;
325 //set first tree file as new current treefile
326 string currentTree = "";
327 itTypes = outputTypes.find("tree");
328 if (itTypes != outputTypes.end()) {
329 if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
332 m->mothurOutEndLine();
333 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
334 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
335 m->mothurOutEndLine();
340 catch(exception& e) {
341 m->errorOut(e, "ClearcutCommand", "execute");
345 /**************************************************************************************/