}
}
//**********************************************************************************************************************
+string ShhherCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "shhh.fasta"; }
+ else if (type == "name") { outputFileName = "shhh.names"; }
+ else if (type == "group") { outputFileName = "shhh.groups"; }
+ else if (type == "counts") { outputFileName = "shhh.counts"; }
+ else if (type == "qfile") { outputFileName = "shhh.qual"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ShhherCommand::ShhherCommand(){
try {
setParameters();
//initialize outputTypes
-// vector<string> tempOutNames;
-// outputTypes["pn.dist"] = tempOutNames;
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["counts"] = tempOutNames;
+ outputTypes["qfile"] = tempOutNames;
}
catch(exception& e) {
}
//initialize outputTypes
- vector<string> tempOutNames;
-// outputTypes["pn.dist"] = tempOutNames;
- // outputTypes["fasta"] = tempOutNames;
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["counts"] = tempOutNames;
+ outputTypes["qfile"] = 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(compositeFASTAFileName != ""){
- outputNames.push_back(compositeFASTAFileName);
- outputNames.push_back(compositeNamesFileName);
+ outputNames.push_back(compositeFASTAFileName); outputTypes["fasta"].push_back(compositeFASTAFileName);
+ outputNames.push_back(compositeNamesFileName); outputTypes["name"].push_back(compositeNamesFileName);
}
m->mothurOutEndLine();
duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
}
- string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+ string nameFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
ofstream nameFile;
m->openOutputFile(nameFileName, nameFile);
float intensity;
- flowFile >> numFlowCells;
+ string numFlowTest;
+ flowFile >> numFlowTest;
+
+ if (!m->isContainingOnlyDigits(numFlowTest)) { m->mothurOut("[ERROR]: expected a number and got " + numFlowTest + ", quitting. Did you use the flow parameter instead of the file parameter?"); m->mothurOutEndLine(); exit(1); }
+ else { convert(numFlowTest, numFlowCells); }
+
int index = 0;//pcluster
while(!flowFile.eof()){
try {
ReadMatrix* read = new ReadColumnMatrix(distFileName);
- read->setCutoff(cutoff);
-
- NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
- clusterNameMap->readMap();
- read->read(clusterNameMap);
-
- ListVector* list = read->getListVector();
- SparseMatrix* matrix = read->getMatrix();
+ read->setCutoff(cutoff);
+
+ NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
+ clusterNameMap->readMap();
+ read->read(clusterNameMap);
- delete read;
- delete clusterNameMap;
+ ListVector* list = read->getListVector();
+ SparseDistanceMatrix* matrix = read->getDMatrix();
+
+ delete read;
+ delete clusterNameMap;
RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.qual";
+ string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile");
ofstream qualityFile;
m->openOutputFile(qualityFileName, qualityFile);
}
}
qualityFile.close();
- outputNames.push_back(qualityFileName);
+ outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName);
}
catch(exception& e) {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.fasta";
+ string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
ofstream fastaFile;
m->openOutputFile(fastaFileName, fastaFile);
}
fastaFile.close();
- outputNames.push_back(fastaFileName);
+ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
if(compositeFASTAFileName != ""){
m->appendFiles(fastaFileName, compositeFASTAFileName);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.names";
+ string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
ofstream nameFile;
m->openOutputFile(nameFileName, nameFile);
}
}
nameFile.close();
- outputNames.push_back(nameFileName);
+ outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
if(compositeNamesFileName != ""){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
- string groupFileName = fileRoot + "shhh.groups";
+ string fileRoot = m->getRootName(m->getSimpleName(flowFileName));
+ int pos = fileRoot.find_first_of('.');
+ string fileGroup = fileRoot;
+ if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); }
+ string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group");
ofstream groupFile;
m->openOutputFile(groupFileName, groupFile);
for(int i=0;i<numSeqs;i++){
if (m->control_pressed) { break; }
- groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
+ groupFile << seqNameVector[i] << '\t' << fileGroup << endl;
}
groupFile.close();
- outputNames.push_back(groupFileName);
+ outputNames.push_back(groupFileName); outputTypes["group"].push_back(groupFileName);
}
catch(exception& e) {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(flowFileName); }
- string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.counts";
+ string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) +getOutputFileNameTag("counts");
ofstream otuCountsFile;
m->openOutputFile(otuCountsFileName, otuCountsFile);
}
}
otuCountsFile.close();
- outputNames.push_back(otuCountsFileName);
+ outputNames.push_back(otuCountsFileName); outputTypes["counts"].push_back(otuCountsFileName);
}
catch(exception& e) {
int ShhherCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
getSingleLookUp(); if (m->control_pressed) { return 0; }
getJointLookUp(); if (m->control_pressed) { return 0; }
#endif
if(compositeFASTAFileName != ""){
- outputNames.push_back(compositeFASTAFileName);
- outputNames.push_back(compositeNamesFileName);
+ outputNames.push_back(compositeFASTAFileName); outputTypes["fasta"].push_back(compositeFASTAFileName);
+ outputNames.push_back(compositeNamesFileName); outputTypes["name"].push_back(compositeNamesFileName);
}
m->mothurOutEndLine();
//Windows version shared memory, so be careful when passing variables through the shhhFlowsData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
//////////////////////////////////////////////////////////////////////////////////////////////////////
-
+ /*
vector<shhhFlowsData*> pDataArray;
DWORD dwThreadIdArray[processors-1];
HANDLE hThreadArray[processors-1];
CloseHandle(hThreadArray[i]);
delete pDataArray[i];
}
-
+ */
#endif
for (int i=0;i<processIDS.size();i++) {
if (m->control_pressed) { break; }
vector<int> otuCounts(numOTUs, 0);
- for(int i=0;i<numSeqs;i++) { otuCounts[otuData[i]]++; }
+ for(int j=0;j<numSeqs;j++) { otuCounts[otuData[j]]++; }
calcCentroidsDriver(numOTUs, cumNumSeqs, nSeqsPerOTU, seqIndex, change, centroids, singleTau, mapSeqToUnique, uniqueFlowgrams, flowDataIntI, lengths, numFlowCells, seqNumber);
if ((large) && (g == 0)) { flowFileName = filenames[i]; theseFlowFileNames[0] = filenames[i]; }
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir = m->hasPath(flowFileName); }
- string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.qual";
- string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.fasta";
- string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.names";
- string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + "shhh.counts";
- string fileRoot = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName));
- string groupFileName = fileRoot + "shhh.groups";
+ string qualityFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("qfile");
+ string fastaFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("fasta");
+ string nameFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("name");
+ string otuCountsFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("counts");
+ string fileRoot = m->getRootName(m->getSimpleName(flowFileName));
+ int pos = fileRoot.find_first_of('.');
+ string fileGroup = fileRoot;
+ if (pos != string::npos) { fileGroup = fileRoot.substr(pos+1, (fileRoot.length()-1-(pos+1))); }
+ string groupFileName = thisOutputDir + fileRoot + getOutputFileNameTag("group");
writeQualities(numOTUs, numFlowCells, qualityFileName, otuCounts, nSeqsPerOTU, seqNumber, singleTau, flowDataIntI, uniqueFlowgrams, cumNumSeqs, mapUniqueToSeq, seqNameVector, centroids, aaI); if (m->control_pressed) { break; }
writeSequences(thisCompositeFASTAFileName, numOTUs, numFlowCells, fastaFileName, otuCounts, uniqueFlowgrams, seqNameVector, aaI, centroids);if (m->control_pressed) { break; }
writeNames(thisCompositeNamesFileName, numOTUs, nameFileName, otuCounts, seqNameVector, aaI, nSeqsPerOTU); if (m->control_pressed) { break; }
writeClusters(otuCountsFileName, numOTUs, numFlowCells,otuCounts, centroids, uniqueFlowgrams, seqNameVector, aaI, nSeqsPerOTU, lengths, flowDataIntI); if (m->control_pressed) { break; }
- writeGroups(groupFileName, fileRoot, numSeqs, seqNameVector); if (m->control_pressed) { break; }
+ writeGroups(groupFileName, fileGroup, numSeqs, seqNameVector); if (m->control_pressed) { break; }
if (large) {
if (g > 0) {
- m->appendFiles(qualityFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.qual"));
+ m->appendFiles(qualityFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("qfile")));
m->mothurRemove(qualityFileName);
- m->appendFiles(fastaFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.fasta"));
+ m->appendFiles(fastaFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("fasta")));
m->mothurRemove(fastaFileName);
- m->appendFiles(nameFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.names"));
+ m->appendFiles(nameFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("name")));
m->mothurRemove(nameFileName);
- m->appendFiles(otuCountsFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.counts"));
+ m->appendFiles(otuCountsFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("counts")));
m->mothurRemove(otuCountsFileName);
- m->appendFiles(groupFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + "shhh.groups"));
+ m->appendFiles(groupFileName, (thisOutputDir + m->getRootName(m->getSimpleName(theseFlowFileNames[0])) + getOutputFileNameTag("group")));
m->mothurRemove(groupFileName);
}
m->mothurRemove(theseFlowFileNames[g]);
thisFlowDataIntI.clear();
thisNameMap.clear();
- flowFile >> numFlowCells;
+ string numFlowTest;
+ flowFile >> numFlowTest;
+
+ if (!m->isContainingOnlyDigits(numFlowTest)) { m->mothurOut("[ERROR]: expected a number and got " + numFlowTest + ", quitting. Did you use the flow parameter instead of the file parameter?"); m->mothurOutEndLine(); exit(1); }
+ else { convert(numFlowTest, numFlowCells); }
+
if (m->debug) { m->mothurOut("[DEBUG]: numFlowCells = " + toString(numFlowCells) + ".\n"); }
int index = 0;//pcluster
while(!flowFile.eof()){
read->read(clusterNameMap);
ListVector* list = read->getListVector();
- SparseMatrix* matrix = read->getMatrix();
+ SparseDistanceMatrix* matrix = read->getDMatrix();
delete read;
delete clusterNameMap;
}
}
qualityFile.close();
- outputNames.push_back(qualityFileName);
+ outputNames.push_back(qualityFileName); outputTypes["qfile"].push_back(qualityFileName);
}
catch(exception& e) {
}
fastaFile.close();
- outputNames.push_back(fastaFileName);
+ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
if(thisCompositeFASTAFileName != ""){
m->appendFiles(fastaFileName, thisCompositeFASTAFileName);
}
}
nameFile.close();
- outputNames.push_back(nameFileName);
+ outputNames.push_back(nameFileName); outputTypes["name"].push_back(nameFileName);
if(thisCompositeNamesFileName != ""){
groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
}
groupFile.close();
- outputNames.push_back(groupFileName);
+ outputNames.push_back(groupFileName); outputTypes["group"].push_back(groupFileName);
}
catch(exception& e) {
}
}
otuCountsFile.close();
- outputNames.push_back(otuCountsFileName);
+ outputNames.push_back(otuCountsFileName); outputTypes["counts"].push_back(otuCountsFileName);
}
catch(exception& e) {