OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("classify.seqs");
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
#endif
ifstream in;
- 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--;
#endif
ifstream in;
- ableToOpen = openInputFile(namefileNames[i], in);
+ ableToOpen = openInputFile(namefileNames[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(namefileNames[i]);
+ m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ namefileNames[i] = tryPath;
+ }
+ }
in.close();
#ifdef USE_MPI
}
#endif
- if (ableToOpen == 1) { m->mothurOut("Unable to match name file with fasta file."); m->mothurOutEndLine(); abort = true; }
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + namefileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); abort = true;
+ //erase from file list
+ namefileNames.erase(namefileNames.begin()+i);
+ i--;
+ }
+
}
}
#endif
ifstream in;
- ableToOpen = openInputFile(groupfileNames[i], in);
+ ableToOpen = openInputFile(groupfileNames[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(groupfileNames[i]);
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ groupfileNames[i] = tryPath;
+ }
+ }
in.close();
#ifdef USE_MPI
}
#endif
- if (ableToOpen == 1) { m->mothurOut("Unable to match group file with fasta file, not using " + groupfileNames[i] + "."); m->mothurOutEndLine(); groupfileNames[i] = ""; }
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + groupfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); groupfileNames[i] = "";
+ //erase from file list
+ groupfileNames.erase(groupfileNames.begin()+i);
+ i--;
+ }
}
}
#ifdef USE_MPI
int pid, end, numSeqsPerProcessor;
int tag = 2001;
- vector<long> MPIPos;
+ vector<unsigned long int> MPIPos;
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
}
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] == '>'){ 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();
numFastaSeqs = positions.size();
int numSeqsPerProcessor = numFastaSeqs / processors;
-
+
for (int i = 0; i < processors; i++) {
- int startPos = positions[ i * numSeqsPerProcessor ];
+ unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
if(i == processors - 1){
numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
}
for(int i=0;i<line->numSeqs;i++){
if (m->control_pressed) { return 0; }
-
- Sequence* candidateSeq = new Sequence(inFASTA);
-
+
+ Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+
if (candidateSeq->getName() != "") {
taxonomy = classify->getTaxonomy(candidateSeq);
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<long>& MPIPos){
+int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& newFile, MPI_File& tempFile, vector<unsigned long int>& MPIPos){
try {
MPI_Status statusNew;
MPI_Status statusTemp;