]> git.donarmstrong.com Git - mothur.git/blobdiff - unifracunweightedcommand.cpp
added get.otus and remove.otus commands
[mothur.git] / unifracunweightedcommand.cpp
index 28bc2ac55f64ebb02185a55d43ba9ea8e6faa03b..b80a3abb4bb76bd0a5da3afa5548df0771797e45 100644 (file)
@@ -9,6 +9,59 @@
 
 #include "unifracunweightedcommand.h"
 
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"groups","iters","distance","random", "processors","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracUnweightedCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+UnifracUnweightedCommand::UnifracUnweightedCommand(){  
+       try {
+               globaldata = GlobalData::getInstance();
+               abort = true;
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["unweighted"] = tempOutNames;
+               outputTypes["uwsummary"] = tempOutNames;
+               outputTypes["phylip"] = tempOutNames;
+               outputTypes["column"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getRequiredParameters(){      
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracUnweightedCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::getRequiredFiles(){   
+       try {
+               string Array[] =  {"tree","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "UnifracUnweightedCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 /***********************************************************/
 UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
        try {
@@ -21,7 +74,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"groups","iters","distance","random", "outputdir","inputdir"};
+                       string Array[] =  {"groups","iters","distance","random", "processors","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -34,13 +87,20 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["unweighted"] = tempOutNames;
+                       outputTypes["uwsummary"] = tempOutNames;
+                       outputTypes["phylip"] = tempOutNames;
+                       outputTypes["column"] = tempOutNames;
+                       
                        if (globaldata->gTree.size() == 0) {//no trees were read
                                m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.unweighted command."); m->mothurOutEndLine(); abort = true;  }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
                                                        
                        //check for optional parameter and set defaults
@@ -48,34 +108,41 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
                        itersString = validParameter.validFile(parameters, "iters", false);                             if (itersString == "not found") { itersString = "1000"; }
                        convert(itersString, iters); 
                        
-                       string temp = validParameter.validFile(parameters, "distance", false);                  if (temp == "not found") { temp = "false"; }
-                       phylip = isTrue(temp);
+                       string temp = validParameter.validFile(parameters, "distance", false);                  
+                       if (temp == "not found") { phylip = false; outputForm = ""; }
+                       else{
+                               if ((temp == "lt") || (temp == "column") || (temp == "square")) {  phylip = true;  outputForm = temp; }
+                               else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
+                       }
+                       
+                       temp = validParameter.validFile(parameters, "random", false);                                   if (temp == "not found") { temp = "f"; }
+                       random = m->isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "random", false);                                   if (temp == "not found") { temp = "true"; }
-                       random = isTrue(temp);
+                       temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
+                       convert(temp, processors); 
                        
                        if (!random) {  iters = 0;  } //turn off random calcs
                        
                        //if user selects distance = true and no groups it won't calc the pairwise
                        if ((phylip) && (Groups.size() == 0)) {
                                groups = "all";
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                
                        if (abort == false) {
                                T = globaldata->gTree;
                                tmap = globaldata->gTreemap;
-                               sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".uwsummary";
-                               outputNames.push_back(sumFile);
-                               openOutputFile(sumFile, outSum);
+                               sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".uwsummary";
+                               outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
+                               m->openOutputFile(sumFile, outSum);
                                
                                util = new SharedUtil();
                                util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");   //sets the groups the user wants to analyze
@@ -101,11 +168,12 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 void UnifracUnweightedCommand::help(){
        try {
                m->mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n");
-               m->mothurOut("The unifrac.unweighted command parameters are groups, iters, distance and random.  No parameters are required.\n");
+               m->mothurOut("The unifrac.unweighted command parameters are groups, iters, distance, processors and random.  No parameters are required.\n");
                m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 1 valid group.\n");
                m->mothurOut("The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
-               m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
-               m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
+               m->mothurOut("The distance parameter allows you to create a distance file from the results. The default is false. You may set distance to lt, square or column.\n");
+               m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is false, meaning compare don't your trees with randomly generated trees.\n");
+               m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
                m->mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
                m->mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
                m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
@@ -125,6 +193,8 @@ int UnifracUnweightedCommand::execute() {
                
                if (abort == true) { return 0; }
                
+               int start = time(NULL);
+               
                userData.resize(numComp,0);  //data[0] = unweightedscore 
                randomData.resize(numComp,0); //data[0] = unweightedscore
                //create new tree with same num nodes and leaves as users
@@ -143,8 +213,9 @@ int UnifracUnweightedCommand::execute() {
                        counter = 0;
                        
                        if (random)  {  
-                               output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted", itersString);
-                               outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
+                               output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted", itersString);
+                               outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
+                               outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
                        }
                        
                        
@@ -154,14 +225,9 @@ int UnifracUnweightedCommand::execute() {
                        utreeScores.resize(numComp);  
                        UWScoreSig.resize(numComp); 
 
-                       userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
-                       
-                       if (m->control_pressed) { 
-                               if (random) { delete output;  }
-                               outSum.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
-                               return 0; 
-                       }
+                       userData = unweighted->getValues(T[i], processors, outputDir);  //userData[0] = unweightedscore
+               
+                       if (m->control_pressed) { if (random) { delete output;  } outSum.close();  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  }return 0; }
                        
                        //output scores for each combination
                        for(int k = 0; k < numComp; k++) {
@@ -171,18 +237,14 @@ int UnifracUnweightedCommand::execute() {
                                //add users score to validscores
                                validScores[userData[k]] = userData[k];
                        }
-                       
+               
                        //get unweighted scores for random trees - if random is false iters = 0
                        for (int j = 0; j < iters; j++) {
+               
                                //we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
-                               randomData = unweighted->getValues(T[i], "", "");
+                               randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
                                
-                               if (m->control_pressed) { 
-                                       if (random) { delete output;  }
-                                       outSum.close();
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
-                                       return 0; 
-                               }
+                               if (m->control_pressed) { if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
                        
                                for(int k = 0; k < numComp; k++) {      
                                        //add trees unweighted score to map of scores
@@ -196,31 +258,30 @@ int UnifracUnweightedCommand::execute() {
                                        //add randoms score to validscores
                                        validScores[randomData[k]] = randomData[k];
                                }
+                               
+                               //report progress
+                               m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();  
                        }
-               
+       
                        for(int a = 0; a < numComp; a++) {
                                float rcumul = 1.0000;
-                               //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
-                               for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) { 
-                                       //make rscoreFreq map and rCumul
-                                       map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
-                                       rCumul[a][it->first] = rcumul;
-                                       //get percentage of random trees with that info
-                                       if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
-                                       else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
-                               }
                                
-                               if (random) {   UWScoreSig[a].push_back(rCumul[a][userData[a]]);        }
-                               else            {       UWScoreSig[a].push_back(0.0);                                           }
+                               if (random) {
+                                       //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+                                       for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) { 
+                                               //make rscoreFreq map and rCumul
+                                               map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
+                                               rCumul[a][it->first] = rcumul;
+                                               //get percentage of random trees with that info
+                                               if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
+                                               else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
+                                       }
+                                       UWScoreSig[a].push_back(rCumul[a][userData[a]]);
+                               }else           {       UWScoreSig[a].push_back(0.0);                                           }
+       
                        }
                        
-                       
-                       if (m->control_pressed) { 
-                               if (random) { delete output;  }
-                               outSum.close();
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
-                               return 0; 
-                       }
+                       if (m->control_pressed) { if (random) { delete output;  } outSum.close(); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0;  }
                        
                        //print output files
                        printUWSummaryFile(i);
@@ -239,6 +300,8 @@ int UnifracUnweightedCommand::execute() {
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }      return 0; }
                
+               m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine();
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
@@ -295,16 +358,16 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) {
                                if (UWScoreSig[a][0] > (1/(float)iters)) {
                                        outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
                                        cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl; 
-                                       m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t" + toString(UWScoreSig[a][0])); m->mothurOutEndLine(); 
+                                       m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t" + toString(UWScoreSig[a][0])+ "\n"); 
                                }else {
                                        outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
                                        cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; 
-                                       m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t<" + toString((1/float(iters)))); m->mothurOutEndLine();
+                                       m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t<" + toString((1/float(iters))) + "\n"); 
                                }
                        }else{
                                outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
                                cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl; 
-                               m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t0.00"); m->mothurOutEndLine();
+                               m->mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t0.00\n");
                        }
                }
                
@@ -317,15 +380,23 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) {
 /***********************************************************/
 void UnifracUnweightedCommand::createPhylipFile(int i) {
        try {
-               string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.dist";
-               outputNames.push_back(phylipFileName);
+               string phylipFileName;
+               if ((outputForm == "lt") || (outputForm == "square")) {
+                       phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.phylip.dist";
+                       outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); 
+               }else { //column
+                       phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.column.dist";
+                       outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); 
+               }
                
                ofstream out;
-               openOutputFile(phylipFileName, out);
-                       
-               //output numSeqs
-               out << globaldata->Groups.size() << endl;
-                       
+               m->openOutputFile(phylipFileName, out);
+               
+               if ((outputForm == "lt") || (outputForm == "square")) {
+                       //output numSeqs
+                       out << globaldata->Groups.size() << endl;
+               }
+               
                //make matrix with scores in it
                vector< vector<float> > dists;  dists.resize(globaldata->Groups.size());
                for (int i = 0; i < globaldata->Groups.size(); i++) {
@@ -336,8 +407,8 @@ void UnifracUnweightedCommand::createPhylipFile(int i) {
                int count = 0;
                for (int r=0; r<globaldata->Groups.size(); r++) { 
                        for (int l = r+1; l < globaldata->Groups.size(); l++) {
-                               dists[r][l] = (1.0 - utreeScores[count][0]);
-                               dists[l][r] = (1.0 - utreeScores[count][0]);
+                               dists[r][l] = utreeScores[count][0];
+                               dists[l][r] = utreeScores[count][0];
                                count++;
                        }
                }
@@ -349,11 +420,30 @@ void UnifracUnweightedCommand::createPhylipFile(int i) {
                        if (name.length() < 10) { //pad with spaces to make compatible
                                while (name.length() < 10) {  name += " ";  }
                        }
-                       out << name << '\t';
                        
-                       //output distances
-                       for (int l = 0; l < r; l++) {   out  << dists[r][l] << '\t';  }
-                       out << endl;
+                       if (outputForm == "lt") {
+                               out << name << '\t';
+                       
+                               //output distances
+                               for (int l = 0; l < r; l++) {   out  << dists[r][l] << '\t';  }
+                               out << endl;
+                       }else if (outputForm == "square") {
+                               out << name << '\t';
+                               
+                               //output distances
+                               for (int l = 0; l < globaldata->Groups.size(); l++) {   out  << dists[r][l] << '\t';  }
+                               out << endl;
+                       }else{
+                               //output distances
+                               for (int l = 0; l < r; l++) {   
+                                       string otherName = globaldata->Groups[l];
+                                       if (otherName.length() < 10) { //pad with spaces to make compatible
+                                               while (otherName.length() < 10) {  otherName += " ";  }
+                                       }
+                                       
+                                       out  << name << '\t' << otherName << dists[r][l] << endl;  
+                               }
+                       }
                }
                out.close();
        }