shhh.seqs and trim.flows modifications.

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 7768fa74f1d58fa4f5e15f1031c6046a5bccb58f..14eee605880e3dfa61333cc8eb437f23f7c3d6c5 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -171,7 +171,15 @@ ShhherCommand::ShhherCommand(string option) {
                                m->mothurOutEndLine();
                                abort = true; 
                        }
-                       else if (flowFileName == "not open" || flowFilesFileName == "not open") { abort = true; }       
+                       else if (flowFileName == "not open" || flowFilesFileName == "not open") { abort = true; }
+                       
+                       if(flowFileName != "not found"){        compositeFASTAFileName = "";    }
+                       else{
+                               compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "pn.fasta";
+                               ofstream temp;
+                               m->openOutputFile(compositeFASTAFileName, temp);
+                               temp.close();
+                       }
                        
                        //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"){  
@@ -326,9 +334,7 @@ int ShhherCommand::execute(){
                                
                                cout << "\nClustering flowgrams..." << endl;
                                string listFileName = cluster(distFileName, namesFileName);
-       //                      string listFileName = "PriestPot_C7.pn.list";
-       //                      string listFileName = "test.mock_rep3.v69.pn.list";
-                       
+
                                getOTUData(listFileName);
                                initPyroCluster();
 
@@ -1992,7 +1998,6 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
 
 void ShhherCommand::writeSequences(vector<int> otuCounts){
        try {
-               
                string bases = "TACG";
                
                string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.fasta";
@@ -2018,6 +2023,10 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
                        }
                }
                fastaFile.close();
+               
+               if(compositeFASTAFileName != ""){
+                       m->appendFiles(fastaFileName, compositeFASTAFileName);
+               }
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "writeSequences");