X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimseqscommand.cpp;h=9f8fafb24e14a807baa8dd5a981c93556c46e3b7;hb=791f42d21a85f794529fd4c912dcc27d873c25e8;hp=9913727dcdc8257816e1f83fab2f8a4b903ff1cd;hpb=fc3b1fc4fc1c4e38fde6b0c0ee7896b5fe0b9d57;p=mothur.git

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 9913727..9f8fafb 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -329,6 +329,8 @@ int TrimSeqsCommand::execute(){
 		
 		numFPrimers = 0;  //this needs to be initialized
 		numRPrimers = 0;
+        numSpacers = 0;
+        numLinkers = 0;
 		createGroup = false;
 		vector<vector<string> > fastaFileNames;
 		vector<vector<string> > qualFileNames;
@@ -435,6 +437,17 @@ int TrimSeqsCommand::execute(){
 					
 					Sequence currSeq(in); m->gobble(in);
 					out << currSeq.getName() << '\t' << it->second << endl;
+                    
+                    if (nameFile != "") {
+                        map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                        if (itName != nameMap.end()) { 
+                            vector<string> thisSeqsNames; 
+                            m->splitAtChar(itName->second, thisSeqsNames, ',');
+                            for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+                                out << thisSeqsNames[k] << '\t' << it->second << endl;
+                            }
+                        }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }							
+                    }
 				}
 				in.close();
 				out.close();
@@ -746,7 +759,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 				count++;
 			}
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = inFASTA.tellg();
 				if ((pos == -1) || (pos >= line.end)) { break; }
 			
@@ -786,7 +799,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 		int exitCommand = 1;
 		processIDS.clear();
 		
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				//loop through and create all the processes you want
 		while (process != processors) {
 			int pid = fork();
@@ -1027,7 +1040,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 				}
 			}
 			
-            #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+            #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			if(createGroup){
 				ifstream in;
 				string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
@@ -1067,7 +1080,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
         vector<unsigned long long> fastaFilePos;
 		vector<unsigned long long> qfileFilePos;
 		
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		//set file positions for fasta file
 		fastaFilePos = m->divideFile(filename, processors);
 		
@@ -1157,6 +1170,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
         }else{
             int numFastaSeqs = 0;
             fastaFilePos = m->setFilePosFasta(filename, numFastaSeqs); 
+            if (fastaFilePos.size() < processors) { processors = fastaFilePos.size(); }
         
             if (qfilename != "") { 
                 int numQualSeqs = 0;
@@ -1176,9 +1190,8 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
                 cout << fastaFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
                 if (qfilename != "") {  qLines.push_back(linePair(qfileFilePos[startIndex], numSeqsPerProcessor)); }
             }
-        
-            if(qfilename == "")	{	qLines = lines;	} //files with duds
         }
+            if(qfilename == "")	{	qLines = lines;	} //files with duds
 			return 1;
 		
 		#endif
@@ -1242,9 +1255,10 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
 					primerNameVector.push_back(group);
 				}
 				else if(type == "REVERSE"){
-					Sequence oligoRC("reverse", oligo);
-					oligoRC.reverseComplement();
-					revPrimer.push_back(oligoRC.getUnaligned());
+					//Sequence oligoRC("reverse", oligo);
+					//oligoRC.reverseComplement();
+                    string oligoRC = reverseOligo(oligo);
+					revPrimer.push_back(oligoRC);
 				}
 				else if(type == "BARCODE"){
 					inOligos >> group;
@@ -1467,6 +1481,46 @@ bool TrimSeqsCommand::cullHomoP(Sequence& seq){
 	}
 	
 }
+//********************************************************************/
+string TrimSeqsCommand::reverseOligo(string oligo){
+	try {
+        string reverse = "";
+        
+        for(int i=oligo.length()-1;i>=0;i--){
+            
+            if(oligo[i] == 'A')		{	reverse += 'T';	}
+            else if(oligo[i] == 'T'){	reverse += 'A';	}
+            else if(oligo[i] == 'U'){	reverse += 'A';	}
+            
+            else if(oligo[i] == 'G'){	reverse += 'C';	}
+            else if(oligo[i] == 'C'){	reverse += 'G';	}
+            
+            else if(oligo[i] == 'R'){	reverse += 'Y';	}
+            else if(oligo[i] == 'Y'){	reverse += 'R';	}
+            
+            else if(oligo[i] == 'M'){	reverse += 'K';	}
+            else if(oligo[i] == 'K'){	reverse += 'M';	}
+            
+            else if(oligo[i] == 'W'){	reverse += 'W';	}
+            else if(oligo[i] == 'S'){	reverse += 'S';	}
+            
+            else if(oligo[i] == 'B'){	reverse += 'V';	}
+            else if(oligo[i] == 'V'){	reverse += 'B';	}
+            
+            else if(oligo[i] == 'D'){	reverse += 'H';	}
+            else if(oligo[i] == 'H'){	reverse += 'D';	}
+            
+            else						{	reverse += 'N';	}
+        }
+        
+        
+        return reverse;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "TrimSeqsCommand", "reverseOligo");
+		exit(1);
+	}
+}
 
 //***************************************************************************************************************