filename = getRootName(filename);
filename = filename + "shared";
openOutputFile(filename, out);
+
+ groupMap = globaldata->gGroupmap;
+
+ //fill filehandles with neccessary ofstreams
+ int i;
+ ofstream* temp;
+ for (i=0; i<groupMap->getNumGroups(); i++) {
+ temp = new ofstream;
+ filehandles[groupMap->namesOfGroups[i]] = temp;
+ }
+
+ //set fileroot
+ fileroot = getRootName(globaldata->getListFile());
+
+ //clears file before we start to write to it below
+ for (int i=0; i<groupMap->getNumGroups(); i++) {
+ remove((fileroot + groupMap->namesOfGroups[i] + ".rabund").c_str());
+ }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function SharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedCommand", "SharedCommand");
exit(1);
}
-
}
//**********************************************************************************************************************
int SharedCommand::execute(){
try {
- globaldata = GlobalData::getInstance();
+
+ //lookup.clear();
+ string errorOff = "no error";
//read in listfile
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
+ delete read;
+
input = globaldata->ginput;
- list = globaldata->glist;
-
- shared = new Shared();
- int i = 0;
- while(list != NULL){
- shared->getSharedVectors(i, list); //fills sharedGroups with new info and updates sharedVector
- list = input->getListVector(); //get new list vector to process
- printSharedData(); //prints info to the .shared file
- i++;
+ SharedList = globaldata->gSharedList;
+ string lastLabel = SharedList->getLabel();
+ vector<SharedRAbundVector*> lookup;
+
+ if (SharedList->getNumSeqs() != groupMap->getNumSeqs()) {
+ mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine();
+
+ out.close();
+ remove(filename.c_str()); //remove blank shared file you made
+
+ createMisMatchFile();
+
+ //delete memory
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
+ }
+ delete SharedList;
+ globaldata->gSharedList = NULL;
+
+ return 1;
+ }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+
+
+ while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+
+
+ if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+
+ lookup = SharedList->getSharedRAbundVector();
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ processedLabels.insert(SharedList->getLabel());
+ userLabels.erase(SharedList->getLabel());
+ }
+
+ if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete SharedList;
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ processedLabels.insert(SharedList->getLabel());
+ userLabels.erase(SharedList->getLabel());
+ }
+
+
+ lastLabel = SharedList->getLabel();
+
+ delete SharedList;
+ SharedList = input->getSharedListVector(); //get new list vector to process
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ if (processedLabels.count(lastLabel) != 1) {
+ needToRun = true;
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (SharedList != NULL) { delete SharedList; }
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ delete SharedList;
+ }
+
+ globaldata->gSharedList = NULL;
+
+ out.close();
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
}
+
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//**********************************************************************************************************************
-void SharedCommand::printSharedData() {
+void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
try {
- //prints out horizontally
- for (it = shared->sharedGroups.begin(); it != shared->sharedGroups.end(); it++) {
- out << it->second->getLabel() << "\t" << it->first << "\t"; //prints out label and groupname
- it->second->print(out); // prints sharedrabundvector
+
+ //initialize bin values
+ for (int i = 0; i < thislookup.size(); i++) {
+ out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+ thislookup[i]->print(out);
+
+ RAbundVector rav = thislookup[i]->getRAbundVector();
+ openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+ rav.print(*(filehandles[thislookup[i]->getGroup()]));
+ (*(filehandles[thislookup[i]->getGroup()])).close();
}
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SharedCommand class Function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SharedCommand", "printSharedData");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SharedCommand class function printSharedData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+void SharedCommand::createMisMatchFile() {
+ try {
+ ofstream outMisMatch;
+ string outputMisMatchName = getRootName(globaldata->inputFileName);
+
+ //you have sequences in your list file that are not in your group file
+ if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) {
+ outputMisMatchName += "missing.group";
+ mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+
+ openOutputFile(outputMisMatchName, outMisMatch);
+
+ //go through list and if group returns "not found" output it
+ for (int i = 0; i < SharedList->getNumBins(); i++) {
+
+ string names = SharedList->get(i);
+
+ while (names.find_first_of(',') != -1) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+ string group = groupMap->getGroup(name);
+
+ if(group == "not found") { outMisMatch << name << endl; }
+ }
+
+ //get last name
+ string group = groupMap->getGroup(names);
+ if(group == "not found") { outMisMatch << names << endl; }
+ }
+
+ outMisMatch.close();
+
+
+ }else {//you have sequences in your group file that are not in you list file
+
+ outputMisMatchName += "missing.name";
+ mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+
+ map<string, string> namesInList;
+
+ //go through listfile and get names
+ for (int i = 0; i < SharedList->getNumSeqs(); i++) {
+
+ string names = SharedList->get(i);
+
+ while (names.find_first_of(',') != -1) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+
+ namesInList[name] = name;
+ }
+
+ //get last name
+ namesInList[names] = names;
+ }
+
+ //get names of sequences in groupfile
+ vector<string> seqNames = groupMap->getNamesSeqs();
+
+ map<string, string>::iterator itMatch;
+
+ openOutputFile(outputMisMatchName, outMisMatch);
+
+ //loop through names in seqNames and if they aren't in namesIn list output them
+ for (int i = 0; i < seqNames.size(); i++) {
+
+ itMatch = namesInList.find(seqNames[i]);
+
+ if (itMatch == namesInList.end()) {
+
+ outMisMatch << seqNames[i] << endl;
+ }
+ }
+ outMisMatch.close();
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "SharedCommand", "createMisMatchFile");
exit(1);
}
-
}
//**********************************************************************************************************************
SharedCommand::~SharedCommand(){
//delete list;
- delete read;
+
+
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff