ShhherCommand::ShhherCommand(string option) {
try {
+
+#ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
+
+ if(pid == 0){
+#endif
abort = false; calledHelp = false;
//allow user to run help
if (path == "") { parameters["file"] = inputDir + it->second; }
}
}
-
-
+
+ //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 = ""; }
+
//check for required parameters
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;
}
}
else{
ofstream temp;
-
+
+ string thisoutputDir = m->hasPath(flowFilesFileName); //if user entered a file with a path then preserve it
+
//flow.files = 9 character offset
- compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
+ compositeFASTAFileName = thisoutputDir + m->getRootName(m->getSimpleName(flowFilesFileName)) + "shhh.fasta";
m->openOutputFile(compositeFASTAFileName, temp);
temp.close();
- compositeNamesFileName = 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{
+ if (outputDir == "") { outputDir = m->hasPath(flowFileName); }
flowFileVector.push_back(flowFileName);
}
-
-
- //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(flowFileName); //if user entered a file with a path then preserve it
- }
-
-
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string temp;
}
}
+#ifdef USE_MPI
+ }
+#endif
}
catch(exception& e) {
m->errorOut(e, "ShhherCommand", "ShhherCommand");
int tag = 1976;
MPI_Status status;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
- MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
-
+
if(pid == 0){
for(int i=1;i<ncpus;i++){
getSingleLookUp(); if (m->control_pressed) { return 0; }
getJointLookUp(); if (m->control_pressed) { return 0; }
+ vector<string> flowFileVector;
+ if(flowFilesFileName != "not found"){
+ string fName;
+
+ ifstream flowFilesFile;
+ m->openInputFile(flowFilesFileName, flowFilesFile);
+ while(flowFilesFile){
+ fName = m->getline(flowFilesFile);
+ flowFileVector.push_back(fName);
+ m->gobble(flowFilesFile);
+ }
+ }
+ else{
+ flowFileVector.push_back(flowFileName);
+ }
+
int numFiles = flowFileVector.size();
for(int i=1;i<ncpus;i++){
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);
}
}
/**************************************************************************************************/
+string ShhherCommand::createNamesFile(){
+ try{
+
+ vector<string> duplicateNames(numUniques, "");
+ for(int i=0;i<numSeqs;i++){
+ duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
+ }
+
+ string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+
+ ofstream nameFile;
+ m->openOutputFile(nameFileName, nameFile);
+
+ for(int i=0;i<numUniques;i++){
+
+ if (m->control_pressed) { break; }
+
+ // nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
+ nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
+ }
+
+ nameFile.close();
+ return nameFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "createNamesFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
try{
if (numFiles < processors) { processors = numFiles; }
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if (processors == 1) { driver(flowFileVector, compositeFASTAFileName, compositeNamesFileName, 0, flowFileVector.size()); }
else { createProcesses(flowFileVector); } //each processor processes one file
#else
lines.push_back(linePair(startIndex, endIndex));
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
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;
if(otuCounts[i] > 0){
qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
-
+
int j=4; //need to get past the first four bases
while(qualities[i][j] != -1){
- qualityFile << qualities[i][j] << ' ';
- j++;
+ qualityFile << qualities[i][j] << ' ';
+ if (j > qualities[i].size()) { break; }
+ j++;
}
qualityFile << endl;
}
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);
projects / mothur.git / blobdiff