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 {
- cout << "creating sharedfile...";
//lookup.clear();
- int count = 1;
string errorOff = "no error";
+ //errorOff = "";
//read in listfile
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
+ delete read;
input = globaldata->ginput;
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;
- set<int> userLines = globaldata->lines;
+ set<string> userLabels = globaldata->labels;
-
- while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+ 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());
- userLines.erase(count);
}
if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = SharedList->getLabel();
+
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());
+
+ //restore real lastlabel to save below
+ SharedList->setLabel(saveLabel);
}
delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
-
- count++;
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- //cout << "Your file does not include the label "<< *it;
if (processedLabels.count(lastLabel) != 1) {
- //cout << ". I will use " << lastList->getLabel() << "." << endl;
needToRun = true;
- }else {
- //cout << ". Please refer to " << lastList->getLabel() << "." << endl;
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- delete SharedList;
+ 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;
- delete read;
out.close();
- cout << "complete." << endl;
+ 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";
- 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";
+ errorOut(e, "SharedCommand", "execute");
exit(1);
}
-
}
//**********************************************************************************************************************
void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
//initialize bin values
for (int i = 0; i < thislookup.size(); i++) {
+//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
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->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());
+
+ 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);
}
-
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff