//#include "uc.h"
#include "sequence.hpp"
#include "referencedb.h"
-
+#include "systemcommand.h"
//**********************************************************************************************************************
vector<string> ChimeraUchimeCommand::setParameters(){
}
}
//**********************************************************************************************************************
+string ChimeraUchimeCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "chimera") { outputFileName = "uchime.chimeras"; }
+ else if (type == "accnos") { outputFileName = "uchime.accnos"; }
+ else if (type == "alns") { outputFileName = "uchime.alns"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraUchimeCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ChimeraUchimeCommand::ChimeraUchimeCommand(){
try {
abort = true; calledHelp = true;
string uchimeCommand;
#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);
int ableToOpen = m->openInputFile(uchimeCommand, in, "no error"); in.close();
- if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uchimeCommand + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; }
- }
+ if(ableToOpen == 1) {
+ m->mothurOut(uchimeCommand + " file does not exist. Checking path... \n");
+ //check to see if uchime is in the path??
+
+ string uLocation = m->findProgramPath("uchime");
+
+
+ ifstream in2;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
+#else
+ ableToOpen = m->openInputFile((uLocation + ".exe"), in2, "no error"); in2.close();
+#endif
+
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; }
+ else { m->mothurOut("Found uchime in your path, using " + uLocation + "\n");uchimeLocation = uLocation; }
+ }else { uchimeLocation = uchimeCommand; }
+
+ uchimeLocation = m->getFullPathName(uchimeLocation);
+ }
}
catch(exception& e) {
m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
int start = time(NULL);
string nameFile = "";
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.chimera";
- string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.accnos";
- string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.alns";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+ string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
+ string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("alns");
string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
//you provided a groupfile
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; }
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];
if (m->control_pressed) { return 0; }
//remove file made for uchime
- m->mothurRemove(filename);
+ if (!m->debug) { m->mothurRemove(filename); }
+ else { m->mothurOut("[DEBUG]: saving file: " + filename + ".\n"); }
//append files
m->appendFiles((outputFName+groups[i]), outputFName); m->mothurRemove((outputFName+groups[i]));
vector<char*> cPara;
- string path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
-
- string uchimeCommand = path;
+ string uchimeCommand = uchimeLocation;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- uchimeCommand += "uchime ";
+ uchimeCommand += " ";
#else
- uchimeCommand += "uchime";
uchimeCommand = "\"" + uchimeCommand + "\"";
#endif
#else
commandString = "\"" + commandString + "\"";
#endif
+ if (m->debug) { m->mothurOut("[DEBUG]: uchime command = " + commandString + ".\n"); }
system(commandString.c_str());
//free memory
// Allocate memory for thread data.
string extension = toString(i) + ".temp";
- uchimeData* tempUchime = new uchimeData(outputFileName+extension, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0, i);
+ 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->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
}
/**************************************************************************************************/
-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();
// 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, 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->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
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