forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 40b3f2683fbdc47770dd3a4292df5ae8cc6fbf75..e28775f016c4e992d2d8f2d23904c93c6e3f74ef 100644 (file)
--- 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(){  
@@ -418,7 +418,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(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);
                        
                        abskew = validParameter.validFile(parameters, "abskew", false); if (abskew == "not found"){     useAbskew = false;  abskew = "1.9";     }else{  useAbskew = true;  }
                        if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; }
@@ -461,12 +461,22 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        path = path.substr(0, (tempPath.find_last_of('m')));
                        
                        string uchimeCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#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);
@@ -544,7 +554,7 @@ 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 +937,15 @@ 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];
@@ -1005,7 +1016,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                path = path.substr(0, (tempPath.find_last_of('m')));
                
                string uchimeCommand = path;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                uchimeCommand += "uchime ";
 #else
                uchimeCommand += "uchime";
@@ -1243,7 +1254,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                
                //uchime_main(numArgs, uchimeParameters); 
                //cout << "commandString = " << commandString << endl;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
                commandString = "\"" + commandString + "\"";
 #endif
@@ -1309,7 +1320,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
                int num = 0;
                vector<string> files;
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)          
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                //break up file into multiple files
                m->divideFile(filename, processors, files);
                
@@ -1472,7 +1483,7 @@ 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();
@@ -1492,7 +1503,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
                        lines.push_back(linePair(startIndex, endIndex));
                }
                
-#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) {
@@ -1551,7 +1562,7 @@ 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, 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);