#include "chimeraccodecommand.h"
#include "ccode.h"
+//**********************************************************************************************************************
+vector<string> ChimeraCcodeCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" };
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ChimeraCcodeCommand::ChimeraCcodeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["mapinfo"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraCcodeCommand::getRequiredParameters(){
+ try {
+ string AlignArray[] = {"template","fasta"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraCcodeCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-
ChimeraCcodeCommand::ChimeraCcodeCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string Array[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir", };
+ string Array[] = {"fasta", "filter", "processors", "window", "template", "mask", "numwanted", "outputdir","inputdir" };
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ vector<string> tempOutNames;
+ outputTypes["chimera"] = tempOutNames;
+ outputTypes["mapinfo"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = m->openInputFile(tryPath, in, "noerror");
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
fastaFileNames[i] = tryPath;
}
}
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
in.close();
if (ableToOpen == 1) {
}
//if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
- outputDir = "";
- outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
- }
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
templatefile = validParameter.validFile(parameters, "template", true);
if (templatefile == "not open") { abort = true; }
int ChimeraCcodeCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; }
templateSeqsLength = chimera->getLength();
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string outputFileName, accnosFileName;
if (maskfile != "") {
outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras";
string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo";
- if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); return 0; }
#ifdef USE_MPI
- int pid, end, numSeqsPerProcessor;
+ int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long int> MPIPos;
MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; }
if (pid == 0) { //you are the root process
string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n";
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; }
}else{ //you are a child process
MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
//align your part
driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; }
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; }
}
//close files
numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
- if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
+ if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; }
}else{
processIDS.resize(0);
if (m->control_pressed) {
remove(outputFileName.c_str());
remove(accnosFileName.c_str());
- for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }
+ for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } outputTypes.clear();
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
delete chimera;
return 0;
#else
numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
- if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); delete chimera; return 0; }
+ if (m->control_pressed) { remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) { delete lines[i]; } outputTypes.clear(); lines.clear(); delete chimera; return 0; }
#endif
delete chimera;
- outputNames.push_back(outputFileName);
- outputNames.push_back(mapInfo);
- outputNames.push_back(accnosFileName);
-
+ outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
+ outputNames.push_back(mapInfo); outputTypes["mapinfo"].push_back(mapInfo);
+ outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
+
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
if (m->control_pressed) { delete candidateSeq; return 1; }
//print results
- bool isChimeric = chimera->print(outMPI, outAccMPI);
+ chimera->print(outMPI, outAccMPI);
}
}
delete candidateSeq;
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
//force parent to wait until all the processes are done
projects / mothur.git / blobdiff