added processors to pre.cluster for mac and windows. Fixed bug in reNameFile function...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index c035b01d689657c233126b5748b303a04a997356..caddc27d9853299e8777998db09da3d148abba62 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -9,7 +9,7 @@
 
 #include "chimerauchimecommand.h"
 #include "deconvolutecommand.h"
-#include "uc.h"
+//#include "uc.h"
 #include "sequence.hpp"
 #include "referencedb.h"
 
@@ -453,7 +453,25 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        
                        if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
                        if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
-
+                       
+                       //look for uchime exe
+                       path = m->argv;
+                       string tempPath = path;
+                       for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+                       path = path.substr(0, (tempPath.find_last_of('m')));
+                       
+                       string uchimeCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       uchimeCommand = path + "uchime";        //      format the database, -o option gives us the ability
+#else
+                       uchimeCommand = path + "uchime.exe";
+#endif
+                       
+                       //test to make sure uchime exists
+                       ifstream in;
+                       uchimeCommand = m->getFullPathName(uchimeCommand);
+                       int ableToOpen = m->openInputFile(uchimeCommand, in, "no error"); in.close();
+                       if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + uchimeCommand + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; }
                }
        }
        catch(exception& e) {
@@ -964,11 +982,23 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam
 
 int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){
        try {
-               
+               //to allow for spaces in the path
+               outputFName = "\"" + outputFName + "\"";
+               filename = "\"" + filename + "\"";
+               alns = "\"" + alns + "\"";
+                               
                vector<char*> cPara;
-               
-               char* tempUchime = new char[8];  
-               strcpy(tempUchime, "./uchime "); 
+       
+               char* tempUchime;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               tempUchime= new char[10];  
+               *tempUchime = '\0';
+               strncat(tempUchime, "./uchime ", 9); 
+#else
+               tempUchime= new char[8]; 
+               *tempUchime = '\0';
+               strncat(tempUchime, "uchime ", 7); 
+#endif
                cPara.push_back(tempUchime);
                
                char* tempIn = new char[8]; 
@@ -1190,15 +1220,23 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                
                char** uchimeParameters;
                uchimeParameters = new char*[cPara.size()];
-               for (int i = 0; i < cPara.size(); i++) {  uchimeParameters[i] = cPara[i];  } 
-               int numArgs = cPara.size();
+               string commandString = "";
+               for (int i = 0; i < cPara.size(); i++) {  uchimeParameters[i] = cPara[i];  commandString += toString(cPara[i]) + " "; } 
+               //int numArgs = cPara.size();
                
-               uchime_main(numArgs, uchimeParameters); 
+               //uchime_main(numArgs, uchimeParameters); 
+               //cout << "commandString = " << commandString << endl;
+               system(commandString.c_str());
                
                //free memory
-               for(int i = 0; i < cPara.size(); i++)  {  delete[] cPara[i];  }
+               for(int i = 0; i < cPara.size(); i++)  {  delete cPara[i];  }
                delete[] uchimeParameters; 
                
+               //remove "" from filenames
+               outputFName = outputFName.substr(1, outputFName.length()-2);
+               filename = filename.substr(1, filename.length()-2);
+               alns = alns.substr(1, alns.length()-2);
+               
                if (m->control_pressed) { return 0; }
                
                //create accnos file from uchime results
@@ -1306,7 +1344,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
                
                
                //append output files
-               for(int i=0;i<processIDS[i];i++){
+               for(int i=0;i<processIDS.size();i++){
                        m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
                        m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
                        
@@ -1398,7 +1436,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
                
                
                //append output files
-               for(int i=0;i<processIDS[i];i++){
+               for(int i=0;i<processIDS.size();i++){
                        m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
                        m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));