Merge remote-tracking branch 'origin/master'

[mothur.git] / chimerauchimecommand.h

diff --git a/chimerauchimecommand.h b/chimerauchimecommand.h
index 659d1ea39963f05a245cda03acf56f3b6e3d10e9..735c97d1269848b94ac5a01926f93e08d1ccd5ef 100644 (file)
--- a/chimerauchimecommand.h
+++ b/chimerauchimecommand.h
@@ -28,9 +28,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "chimera.uchime";              }
        string getCommandCategory()             { return "Sequence Processing"; }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
-       string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\nhttp://www.mothur.org/wiki/Chimera.uchime\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, in press.\n"; }
+    string getOutputPattern(string);   
+       string getCitation() { return "uchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code was donated to the public domain.\nEdgar,R.C., Haas,B.J., Clemente,J.C., Quince,C. and Knight,R. (2011), UCHIME improves sensitivity and speed of chimera detection.  Bioinformatics 27:2194.\nhttp://www.mothur.org/wiki/Chimera.uchime\n"; }
        string getDescription()         { return "detect chimeric sequences"; }
        
        int execute(); 
@@ -47,7 +48,7 @@ private:
        int driver(string, string, string, string, int&);
        int createProcesses(string, string, string, string, int&);
                
-       bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount, hasName;
+       bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract, hasCount, hasName, dups;
        string fastafile, groupfile, templatefile, outputDir, namefile, countfile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract, uchimeLocation;
        int processors;
        
@@ -64,6 +65,7 @@ private:
        int deconvoluteResults(map<string, string>&, string, string, string);
        int driverGroups(string, string, string, string, int, int, vector<string>);
        int createProcessesGroups(string, string, string, string, vector<string>, string, string, string);
+    int prepFile(string filename, string);
 
 
 };
@@ -189,7 +191,7 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
             if (pDataArray->hasCount) { 
                 error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete cparser; return 0; }
             }else {
-               error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; } 
+               error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, true); if ((error == 1) || pDataArray->m->control_pressed) {  delete parser; return 0; } 
             }
                        
                        //int numSeqs = driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
@@ -524,16 +526,31 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
         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);
-       
-               //add reference file
+        string outputFileName = filename.substr(1, filename.length()-2) + ".uchime_formatted";
+        //prepFile(filename.substr(1, filename.length()-2), outputFileName);
+        //prepFile(filename, outputFileName);
+        /******************************************/
+        ifstream in23;
+        pDataArray->m->openInputFile((filename.substr(1, filename.length()-2)), in23);
+        
+        ofstream out23;
+        pDataArray->m->openOutputFile(outputFileName, out23);
+        
+        while (!in23.eof()) {
+            if (pDataArray->m->control_pressed) { break;  }
+            
+            Sequence seq(in23); pDataArray->m->gobble(in23);
+            
+            if (seq.getName() != "") { seq.printSequence(out23); }
+        }
+        in23.close();
+        out23.close();
+        /******************************************/
+        
+        filename = outputFileName;
+        filename = "\"" + filename + "\"";
+        
+        //add reference file
                char* tempRef = new char[5]; 
                //strcpy(tempRef, "--db"); 
                *tempRef = '\0'; strncat(tempRef, "--db", 4);
@@ -542,6 +559,15 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
                //strcpy(tempR, templatefile.c_str());
                *tempR = '\0'; strncat(tempR, templatefile.c_str(), templatefile.length());
                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);
@@ -733,6 +759,8 @@ static DWORD WINAPI MyUchimeSeqsThreadFunction(LPVOID lpParam){
                for (int j = 0; j < cPara.size(); j++) {  uchimeParameters[j] = cPara[j];  commandString += toString(cPara[j]) + " "; } 
                //int numArgs = cPara.size();
                
+        commandString = "\"" + commandString + "\"";
+        
                //uchime_main(numArgs, uchimeParameters); 
                //cout << "commandString = " << commandString << endl;
         if (pDataArray->m->debug) { pDataArray->m->mothurOut("[DEBUG]: uchime command = " + commandString + ".\n"); }