added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 0512be1a70b1d12b0667f5945e4d1acb5b4768d8..2c435cadb11c1bc413b982676ac58082d4683992 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -383,7 +383,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -441,34 +441,34 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        
                        
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
-                       convert(temp, ksize);
+                       m->mothurConvert(temp, ksize);
                                                
                        temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }                       
-                       convert(temp, window);
+                       m->mothurConvert(temp, window);
                        
                        temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
-                       convert(temp, match);
+                       m->mothurConvert(temp, match);
                        
                        temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
-                       convert(temp, mismatch);
+                       m->mothurConvert(temp, mismatch);
                        
                        temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
-                       convert(temp, divR);
+                       m->mothurConvert(temp, divR);
                        
                        temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
-                       convert(temp, minSimilarity);
+                       m->mothurConvert(temp, minSimilarity);
                        
                        temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
-                       convert(temp, minCoverage);
+                       m->mothurConvert(temp, minCoverage);
                        
                        temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
-                       convert(temp, minBS);
+                       m->mothurConvert(temp, minBS);
                        
                        temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
-                       convert(temp, minSNP);
+                       m->mothurConvert(temp, minSNP);
 
                        temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
-                       convert(temp, parents); 
+                       m->mothurConvert(temp, parents); 
                        
                        temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "t"; }
                        realign = m->isTrue(temp); 
@@ -482,27 +482,27 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "blast"; }
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }             
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                         
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
-                       convert(temp, increment);
+                       m->mothurConvert(temp, increment);
                        
                        temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }               
-                       convert(temp, numwanted);
+                       m->mothurConvert(temp, numwanted);
                        
                        blastlocation = validParameter.validFile(parameters, "blastlocation", false);   
                        if (blastlocation == "not found") { blastlocation = ""; }
                        else {
                                //add / to name if needed
                                string lastChar = blastlocation.substr(blastlocation.length()-1);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                if (lastChar != "/") { blastlocation += "/"; }
 #else
                                if (lastChar != "\\") { blastlocation += "\\"; }        
 #endif
                                blastlocation = m->getFullPathName(blastlocation);
                                string formatdbCommand = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                formatdbCommand = blastlocation + "formatdb";   
 #else
                                formatdbCommand = blastlocation + "formatdb.exe";
@@ -515,7 +515,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                                if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
                                
                                string blastCommand = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                blastCommand = blastlocation + "megablast";     
 #else
                                blastCommand = blastlocation + "megablast.exe";
@@ -533,7 +533,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        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; }
 
                        //until we resolve the issue 10-18-11
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
                        //processors=1;
 #endif
@@ -594,13 +594,14 @@ int ChimeraSlayerCommand::execute(){
 #else
                                //break up file
                                vector<unsigned long long> positions; 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                positions = m->divideFile(thisFastaName, processors);
                                for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(linePair(positions[i], positions[(i+1)]));      }
 #else
                                if (processors == 1) {  lines.push_back(linePair(0, 1000)); }
                                else {
                                        positions = m->setFilePosFasta(thisFastaName, numSeqs); 
+                    if (positions.size() < processors) { processors = positions.size(); }
                                        
                                        //figure out how many sequences you have to process
                                        int numSeqsPerProcessor = numSeqs / processors;
@@ -900,6 +901,16 @@ int ChimeraSlayerCommand::deconvoluteResults(SequenceParser* parser, string outp
                map<string, string> uniqueNames = parser->getAllSeqsMap();
                map<string, string>::iterator itUnique;
                int total = 0;
+        
+        if (trimera) { //add in more potential uniqueNames
+            map<string, string> newUniqueNames = uniqueNames;
+            for (map<string, string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) {
+                newUniqueNames[(it->first)+"_LEFT"] = (it->first)+"_LEFT";
+                newUniqueNames[(it->first)+"_RIGHT"] = (it->first)+"_RIGHT";
+            }
+            uniqueNames = newUniqueNames;
+            newUniqueNames.clear();
+        }
                
                //edit accnos file
                ifstream in2; 
@@ -1147,14 +1158,15 @@ string ChimeraSlayerCommand::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];
@@ -1187,7 +1199,7 @@ int ChimeraSlayerCommand::driverGroups(string outputFName, string accnos, string
                        m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine(); 
                        
                        lines.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        int proc = 1;
                        vector<unsigned long long> positions = m->divideFile(thisFastaName, proc);
                        lines.push_back(linePair(positions[0], positions[1]));  
@@ -1244,7 +1256,7 @@ int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accno
                        breakUp.push_back(thisFileToPriority);
                }
                                
-#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();
@@ -1447,7 +1459,7 @@ int ChimeraSlayerCommand::driver(linePair filePos, string outputFName, string fi
                                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 >= filePos.end)) { break; }
                        #else
@@ -1628,7 +1640,7 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                int num = 0;
                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();