X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=7ff3989dea527060934b417de22ef5078df7a074;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=bad4c96b8c74d645208be1158ad11cd2ef924faf;hpb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index bad4c96..7ff3989 100644
--- 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 {
@@ -1583,7 +1616,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 			string extension = toString(i) + ".temp";
 			
 			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->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
 			tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
 			
 			pDataArray.push_back(tempUchime);
@@ -1715,7 +1748,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
 			string extension = toString(i) + ".temp";
 			
 			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->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount);
 			tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
 			
 			pDataArray.push_back(tempUchime);
@@ -1728,7 +1761,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
 		
 		
 		//using the main process as a worker saves time and memory
-		num = driverGroups(parser, outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups);
+		num = driverGroups(outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups);
 		
 		//Wait until all threads have terminated.
 		WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);