flowFileName = validParameter.validFile(parameters, "flow", true);
flowFilesFileName = validParameter.validFile(parameters, "file", true);
if (flowFileName == "not found" && flowFilesFileName == "not found") {
- m->mothurOut("values for either flow or file must be provided for the shhh.seqs command.");
+ m->mothurOut("values for either flow or file must be provided for the shhh.flows command.");
m->mothurOutEndLine();
abort = true;
}
string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
//flow.files = 9 character offset
- compositeFASTAFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+ compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
m->openOutputFile(compositeFASTAFileName, temp);
temp.close();
- compositeNamesFileName = thisoutputDir + flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
+ compositeNamesFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.names";
m->openOutputFile(compositeNamesFileName, temp);
temp.close();
}
if (flowFileVector.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
}
else{
- outputDir += m->hasPath(flowFileName);
+ if (outputDir == "") { outputDir = m->hasPath(flowFileName); }
flowFileVector.push_back(flowFileName);
}
if (m->control_pressed) { break; }
+
+
getOTUData(listFileName);
m->mothurRemove(distFileName);
if (m->control_pressed) { break; }
+
for(int i=1;i<ncpus;i++){
MPI_Send(&numOTUs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
MPI_Send(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
clusterNameMap->readMap();
read->read(clusterNameMap);
-
+
ListVector* list = read->getListVector();
SparseMatrix* matrix = read->getMatrix();
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.qual";
ofstream qualityFile;
void ShhherCommand::writeSequences(string thisCompositeFASTAFileName, int numOTUs, int numFlowCells, string filename, vector<int> otuCounts, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& centroids){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.fasta";
ofstream fastaFile;
m->openOutputFile(fastaFileName, fastaFile);
void ShhherCommand::writeNames(string thisCompositeNamesFileName, int numOTUs, string filename, vector<int> otuCounts, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.names";
ofstream nameFile;
m->openOutputFile(nameFileName, nameFile);
void ShhherCommand::writeGroups(string filename, int numSeqs, vector<string>& seqNameVector){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(filename));
string groupFileName = fileRoot + "shhh.groups";
ofstream groupFile;
void ShhherCommand::writeClusters(string filename, int numOTUs, int numFlowCells, vector<int> otuCounts, vector<int>& centroids, vector<short>& uniqueFlowgrams, vector<string>& seqNameVector, vector<vector<int> >& aaI, vector<int>& nSeqsPerOTU, vector<int>& lengths, vector<short>& flowDataIntI){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(filename); }
+ if (outputDir == "") { thisOutputDir = m->hasPath(filename); }
string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(filename)) + "shhh.counts";
ofstream otuCountsFile;
m->openOutputFile(otuCountsFileName, otuCountsFile);