X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=be0421a73097bc47aa98934ba4ae59a320e02010;hb=791f42d21a85f794529fd4c912dcc27d873c25e8;hp=98976ce39070321aa5b94964c49ebd238cd9b778;hpb=43ed0accfbc2852849e104ff7eccdd2c42acd4ec;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 98976ce..be0421a 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -12,7 +12,7 @@
 //#include "uc.h"
 #include "sequence.hpp"
 #include "referencedb.h"
-
+#include "systemcommand.h"
 
 //**********************************************************************************************************************
 vector<string> ChimeraUchimeCommand::setParameters(){	
@@ -463,16 +463,44 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 			string uchimeCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			uchimeCommand = path + "uchime";	//	format the database, -o option gives us the ability
+            if (m->debug) { 
+                m->mothurOut("[DEBUG]: Uchime location using \"which uchime\" = "); 
+                Command* newCommand = new SystemCommand("which uchime"); m->mothurOutEndLine();
+                newCommand->execute();
+                delete newCommand;
+                m->mothurOut("[DEBUG]: Mothur's location using \"which mothur\" = "); 
+                newCommand = new SystemCommand("which mothur"); m->mothurOutEndLine();
+                newCommand->execute();
+                delete newCommand;
+            }
 #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; }
-		}
+			if(ableToOpen == 1) {	
+                m->mothurOut(uchimeCommand + " file does not exist. Checking path... \n");
+                //check to see if uchime is in the path??
+                
+                string uLocation = m->findProgramPath("uchime");
+                
+                
+                ifstream in2;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+                ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
+#else
+                ableToOpen = m->openInputFile((uLocation + ".exe"), in2, "no error"); in2.close();
+#endif
+
+                if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; } 
+                else {  m->mothurOut("Found uchime in your path, using " + uLocation + "\n");uchimeLocation = uLocation; }
+            }else {  uchimeLocation = uchimeCommand; }
+            
+            uchimeLocation = m->getFullPathName(uchimeLocation);
+        }
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
@@ -544,7 +572,7 @@ int ChimeraUchimeCommand::execute(){
 				int totalSeqs = 0;
 				
 				if(processors == 1)	{	totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups);	}
-				else				{	totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups);			}
+				else				{	totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups, nameFile, groupFile, fastaFileNames[s]);			}
 
 				if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0;	}				
 
@@ -927,14 +955,15 @@ string ChimeraUchimeCommand::getNamesFile(string& inputFile){
 		string inputString = "fasta=" + inputFile;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-		
+		m->mothurCalling = true;
+        
 		Command* uniqueCommand = new DeconvoluteCommand(inputString);
 		uniqueCommand->execute();
 		
 		map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 		
 		delete uniqueCommand;
-		
+		m->mothurCalling = false;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		
 		nameFile = filenames["name"][0];
@@ -999,16 +1028,10 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 				
 		vector<char*> cPara;
 		
-		string 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 = path;
+		string uchimeCommand = uchimeLocation;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-		uchimeCommand += "uchime ";
+		uchimeCommand += " ";
 #else
-		uchimeCommand += "uchime";
 		uchimeCommand = "\"" + uchimeCommand + "\"";
 #endif
 		
@@ -1247,6 +1270,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 #else
 		commandString = "\"" + commandString + "\"";
 #endif
+        if (m->debug) { m->mothurOut("[DEBUG]: uchime command = " + commandString + ".\n"); }
 		system(commandString.c_str());
 		
 		//free memory
@@ -1419,7 +1443,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 			// Allocate memory for thread data.
 			string extension = toString(i) + ".temp";
 			
-			uchimeData* tempUchime = new uchimeData(outputFileName+extension, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0,  i);
+			uchimeData* tempUchime = new uchimeData(outputFileName+extension, uchimeLocation, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0,  i);
 			tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
 			tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
 			
@@ -1472,7 +1496,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 }
 /**************************************************************************************************/
 
-int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector<string> groups) {
+int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector<string> groups, string nameFile, string groupFile, string fastaFile) {
 	try {
 		
 		processIDS.clear();
@@ -1551,7 +1575,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
 			// Allocate memory for thread data.
 			string extension = toString(i) + ".temp";
 			
-			uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastafile, namefile, groupfile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end,  i);
+			uchimeData* tempUchime = new uchimeData(outputFName+extension, uchimeLocation, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end,  i);
 			tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
 			tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);