changed groupfile in classify.seqs to reflect multiple fasta files

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 0538bff07d99ca1266d488a5844fcde49afaf3bc..bdf059c6a063aadfa2256cfe2368d12c7b69bc0e 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -82,9 +82,46 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        }
                        else if (templateFileName == "not open") { abort = true; }      
                        
-                       groupfile = validParameter.validFile(parameters, "group", true);
-                       if (groupfile == "not open") { abort = true; }  
-                       else if (groupfile == "not found") { groupfile = ""; }
+                       groupfile = validParameter.validFile(parameters, "group", false);
+                       if (groupfile == "not found") { groupfile = "";  }
+                       else { 
+                               splitAtDash(groupfile, groupfileNames);
+                               
+                               //go through files and make sure they are good, if not, then disregard them
+                               for (int i = 0; i < groupfileNames.size(); i++) {
+                                       if (inputDir != "") {
+                                               string path = hasPath(groupfileNames[i]);
+                                               //if the user has not given a path then, add inputdir. else leave path alone.
+                                               if (path == "") {       groupfileNames[i] = inputDir + groupfileNames[i];               }
+                                       }
+                                       int ableToOpen;
+                                       
+                                       #ifdef USE_MPI  
+                                               int pid;
+                                               MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+                                               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+                               
+                                               if (pid == 0) {
+                                       #endif
+
+                                       ifstream in;
+                                       ableToOpen = openInputFile(groupfileNames[i], in);
+                                       in.close();
+                                       
+                                       #ifdef USE_MPI  
+                                                       for (int j = 1; j < processors; j++) {
+                                                               MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); 
+                                                       }
+                                               }else{
+                                                       MPI_Status status;
+                                                       MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+                                               }
+                                               
+                                       #endif
+                                       if (ableToOpen == 1) {  m->mothurOut("Unable to match group file with fasta file."); m->mothurOutEndLine(); abort = true;       }
+                                       
+                               }
+                       }
                        
                        fastaFileName = validParameter.validFile(parameters, "fasta", false);
                        if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the classify.seqs command."); m->mothurOutEndLine(); abort = true;  }
@@ -193,6 +230,10 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                                if (namefileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a name file, you must have one for each fasta file."); m->mothurOutEndLine(); }
                        }
                        
+                       if (groupfile != "") {
+                               if (groupfileNames.size() != fastaFileNames.size()) { abort = true; m->mothurOut("If you provide a group file, you must have one for each fasta file."); m->mothurOutEndLine(); }
+                       }
+                       
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        string temp;
@@ -507,7 +548,7 @@ int ClassifySeqsCommand::execute(){
                        m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
                        start = time(NULL);
                        
-                       PhyloSummary taxaSum(taxonomyFileName, groupfile);
+                       PhyloSummary taxaSum(taxonomyFileName, groupfileNames[s]);
                        
                        if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete classify; return 0; }
                        
@@ -527,7 +568,7 @@ int ClassifySeqsCommand::execute(){
                                                m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
                                        }else{
                                                for (int i = 0; i < itNames->second; i++) { 
-                                                       taxaSum.addSeqToTree(name+toString(i), taxon);  //add it as many times as there are identical seqs
+                                                       taxaSum.addSeqToTree(name, taxon);  //add it as many times as there are identical seqs
                                                }
                                        }
                                }
@@ -582,7 +623,6 @@ int ClassifySeqsCommand::execute(){
                        m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                        for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                        m->mothurOutEndLine();
-                       
                }
                
                delete classify;