OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("chimera.slayer");
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
if (pid == 0) {
#endif
- ableToOpen = openInputFile(fastaFileNames[i], in);
+ ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ fastaFileNames[i] = tryPath;
+ }
+ }
in.close();
#ifdef USE_MPI
#endif
if (ableToOpen == 1) {
- m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
convert(temp, minBS);
- temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
+ temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "100"; }
convert(temp, minSNP);
temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
m->mothurOut("The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
- m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
+ m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n");
m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
#ifdef USE_MPI
m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
- m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
+ m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n");
m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false. \n");
m->mothurOut("The chimera.slayer command should be in the following format: \n");
string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras";
string accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.accnos";
- bool hasAccnos = true;
if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
#ifdef USE_MPI
int pid, end, numSeqsPerProcessor;
int tag = 2001;
- vector<long> MPIPos;
- MPIWroteAccnos = false;
+ vector<unsigned long int> MPIPos;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
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()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); delete chimera; return 0; }
- for (int i = 1; i < processors; i++) {
- bool tempResult;
- MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
- if (tempResult != 0) { MPIWroteAccnos = true; }
- }
}else{ //you are a child process
MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
MPIPos.resize(numSeqs+1);
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; }
-
- MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
}
//close files
MPI_File_close(&outMPIAccnos);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
- //delete accnos file if blank
- if (pid == 0) {
- if (!MPIWroteAccnos) {
- hasAccnos = false;
- remove(accnosFileName.c_str());
- }
- }
-
#else
ofstream outHeader;
string tempHeader = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
return 0;
}
- //delete accnos file if its blank
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
-
}else{
- vector<int> positions;
+ vector<unsigned long int> positions;
processIDS.resize(0);
ifstream inFASTA;
while(!inFASTA.eof()){
input = getline(inFASTA);
if (input.length() != 0) {
- if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
}
}
inFASTA.close();
int numSeqsPerProcessor = numSeqs / processors;
for (int i = 0; i < processors; i++) {
- long int startPos = positions[ i * numSeqsPerProcessor ];
+ unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
if(i == processors - 1){
numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
}
createProcesses(outputFileName, fastaFileNames[s], accnosFileName);
rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
+ rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
//append output files
for(int i=1;i<processors;i++){
remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
}
- vector<string> nonBlankAccnosFiles;
- //delete blank accnos files generated with multiple processes
- for(int i=0;i<processors;i++){
- if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
- nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
- }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); }
+ //append output files
+ for(int i=1;i<processors;i++){
+ appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
+ remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
}
- //append accnos files
- if (nonBlankAccnosFiles.size() != 0) {
- rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
-
- for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
- appendFiles(nonBlankAccnosFiles[h], accnosFileName);
- remove(nonBlankAccnosFiles[h].c_str());
- }
- }else{ hasAccnos = false; }
-
if (m->control_pressed) {
remove(outputFileName.c_str());
remove(accnosFileName.c_str());
return 0;
}
- //delete accnos file if its blank
- if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
#endif
appendFiles(outputFileName, tempHeader);
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
outputNames.push_back(outputFileName);
- if (hasAccnos) { outputNames.push_back(accnosFileName); }
+ outputNames.push_back(accnosFileName);
m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
- }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
+int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
try {
MPI_Status status;
int pid;
//cout << "about to print" << endl;
//print results
bool isChimeric = chimera->print(outMPI, outAccMPI);
- if (isChimeric) { MPIWroteAccnos = true; }
-
}
}
delete candidateSeq;
projects / mothur.git / blobdiff