added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index bad4c96b8c74d645208be1158ad11cd2ef924faf..461c3b693c2c79315d1d98263ce55340541496bb 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -1173,24 +1173,18 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 #else
                uchimeCommand = "\"" + uchimeCommand + "\"";
 #endif
-               
-               char* tempUchime;
+        char* tempUchime;
                tempUchime= new char[uchimeCommand.length()+1]; 
                *tempUchime = '\0';
                strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
                cPara.push_back(tempUchime);
                
-               char* tempIn = new char[8]; 
-               *tempIn = '\0'; strncat(tempIn, "--input", 7);
-               //strcpy(tempIn, "--input"); 
-               cPara.push_back(tempIn);
-               char* temp = new char[filename.length()+1];
-               *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
-               //strcpy(temp, filename.c_str());
-               cPara.push_back(temp);
-               
-               //are you using a reference file
+        //are you using a reference file
                if (templatefile != "self") {
+            string outputFileName = filename.substr(1, filename.length()-2) + ".uchime_formatted";
+            prepFile(filename.substr(1, filename.length()-2), outputFileName);
+            filename = outputFileName;
+            filename = "\"" + filename + "\"";
                        //add reference file
                        char* tempRef = new char[5]; 
                        //strcpy(tempRef, "--db"); 
@@ -1202,6 +1196,15 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                        cPara.push_back(tempR);
                }
                
+               char* tempIn = new char[8]; 
+               *tempIn = '\0'; strncat(tempIn, "--input", 7);
+               //strcpy(tempIn, "--input"); 
+               cPara.push_back(tempIn);
+               char* temp = new char[filename.length()+1];
+               *temp = '\0'; strncat(temp, filename.c_str(), filename.length());
+               //strcpy(temp, filename.c_str());
+               cPara.push_back(temp);
+               
                char* tempO = new char[12]; 
                *tempO = '\0'; strncat(tempO, "--uchimeout", 11);
                //strcpy(tempO, "--uchimeout"); 
@@ -1455,6 +1458,8 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                in.close();
                out.close();
                
+        //if (templatefile != "self") {  m->mothurRemove(filename); }
+        
                return num;
        }
        catch(exception& e) {
@@ -1463,6 +1468,34 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
        }
 }
 /**************************************************************************************************/
+//uchime can't handle some of the things allowed in mothurs fasta files. This functions "cleans up" the file.
+int ChimeraUchimeCommand::prepFile(string filename, string output) {
+       try {
+        
+        ifstream in;
+        m->openInputFile(filename, in);
+        
+        ofstream out;
+        m->openOutputFile(output, out);
+        
+        while (!in.eof()) {
+            if (m->control_pressed) { break;  }
+            
+            Sequence seq(in); m->gobble(in);
+            
+            if (seq.getName() != "") { seq.printSequence(out); }
+        }
+        in.close();
+        out.close();
+        
+        return 0;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraUchimeCommand", "prepFile");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
 
 int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename, string accnos, string alns, int& numChimeras) {
        try {