changes to blastdb to make filenames given to blast unique, changes to split.abund...

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 861c4fbf3da78e42313d7e76751efd2f5d05f3bf..c3faab763accf6f7eabde2bf8f769eabb24a69a3 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -27,7 +27,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip","column","name","cutoff","precision","method","splitmethod","taxonomy","taxlevel","showabund","timing","hard","processors","outputdir","inputdir"};
+                       string Array[] =  {"phylip","column","name","cutoff","precision","method","splitmethod","taxonomy","taxlevel","large","showabund","timing","hard","processors","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -125,6 +125,9 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
                        hard = isTrue(temp);
                        
+                       temp = validParameter.validFile(parameters, "large", false);                    if (temp == "not found") { temp = "F"; }
+                       large = isTrue(temp);
+                       
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
                        convert(temp, processors); 
                        
@@ -165,7 +168,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 
 void ClusterSplitCommand::help(){
        try {
-               m->mothurOut("The cluster.split command parameter options are phylip, column, name, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, processors. Phylip or column and name are required.\n");
+               m->mothurOut("The cluster.split command parameter options are phylip, column, name, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, large, processors. Phylip or column and name are required.\n");
                m->mothurOut("The phylip and column parameter allow you to enter your distance file. \n");
                m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
                m->mothurOut("The cutoff parameter allow you to set the distance you want to cluster to, default is 10.0. \n");
@@ -174,6 +177,7 @@ void ClusterSplitCommand::help(){
                m->mothurOut("The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance or classify. \n");
                m->mothurOut("The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n");
                m->mothurOut("The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=1. \n");
+               m->mothurOut("The large parameter allows you to indicate that your distance matrix is too large to fit in RAM.  The default value is false.\n");
                m->mothurOut("The cluster.split command should be in the following format: \n");
                m->mothurOut("cluster.split(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision, splitmethod=yourSplitmethod, taxonomy=yourTaxonomyfile, taxlevel=yourtaxlevel) \n");
                m->mothurOut("Example: cluster.split(column=abrecovery.dist, name=abrecovery.names, method=furthest, cutoff=0.10, precision=1000, splitmethod=classify, taxonomy=abrecovery.silva.slv.taxonomy, taxlevel=5) \n");       
@@ -229,11 +233,12 @@ int ClusterSplitCommand::execute(){
                if (m->control_pressed) { return 0; }
                
                time_t estart = time(NULL);
+               m->mothurOut("Splitting the distance file..."); m->mothurOutEndLine();
                
                //split matrix into non-overlapping groups
                SplitMatrix* split;
-               if (splitmethod == "distance")  {       split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod);                      }
-               else                                                    {       split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod);  }
+               if (splitmethod == "distance")  {       split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod, large);                       }
+               else                                                    {       split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod, large);   }
                
                split->split();
                
@@ -284,6 +289,8 @@ int ClusterSplitCommand::execute(){
                                                ifstream in;
                                                openInputFile(filename, in);
                                                
+                                               in >> tag; gobble(in);
+                                               
                                                while(!in.eof()) {
                                                        string tempName;
                                                        in >> tempName; gobble(in);
@@ -299,7 +306,7 @@ int ClusterSplitCommand::execute(){
                                                
                                                while(!in2.eof()) {
                                                        string tempName;
-                                                       in2 >> tempName; gobble(in);
+                                                       in2 >> tempName; gobble(in2);
                                                        if (labels.count(tempName) == 0) { labels.insert(tempName); }
                                                }
                                                in2.close();
@@ -312,7 +319,12 @@ int ClusterSplitCommand::execute(){
                
                if (m->control_pressed) { for (int i = 0; i < listFileNames.size(); i++) { remove(listFileNames[i].c_str()); } return 0; }
                
+               m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
+               
                //****************** merge list file and create rabund and sabund files ******************************//
+               estart = time(NULL);
+               m->mothurOut("Merging the clustered files..."); m->mothurOutEndLine();
+               
                ListVector* listSingle;
                map<float, int> labelBins = completeListFile(listFileNames, singletonName, labels, listSingle); //returns map of label to numBins
                
@@ -322,7 +334,7 @@ int ClusterSplitCommand::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) - estart) + " seconds to cluster"); m->mothurOutEndLine();
+               m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to merge."); m->mothurOutEndLine();
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -337,7 +349,7 @@ int ClusterSplitCommand::execute(){
        }
 }
 //**********************************************************************************************************************
-map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames, string singleton, set<string> userLabels, ListVector*& listSingle){
+map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames, string singleton, set<string>& userLabels, ListVector*& listSingle){
        try {
                                
                map<float, int> labelBin;
@@ -367,7 +379,7 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
 
                        if ((*it != "unique") && (convertTestFloat(*it, temp) == true)) {       convert(*it, temp);     }
                        else if (*it == "unique")                                                                               {       temp = -1.0;            }
-                       
+                                               
                        orderFloat.push_back(temp);
                        labelBin[temp] = numSingleBins; //initialize numbins 
                }
@@ -571,6 +583,7 @@ int ClusterSplitCommand::createProcesses(vector < vector < map<string, string> >
                                string filename = toString(getpid()) + ".temp";
                                ofstream out;
                                openOutputFile(filename, out);
+                               out << tag << endl;
                                for (int j = 0; j < listFileNames.size(); j++) { out << listFileNames[j] << endl;  }
                                out.close();