try {
//lookup.clear();
- int count = 1;
string errorOff = "no error";
//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;
- 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() + "\t" + toString(count)); mothurOutEndLine();
+ 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)) {
SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
lookup = SharedList->getSharedRAbundVector();
- mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ 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;
SharedList = input->getSharedListVector(); //get new list vector to process
-
- count++;
}
//output error messages about any remaining user labels
}
}
- //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() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
globaldata->gSharedList = NULL;
- delete read;
out.close();
exit(1);
}
}
+//**********************************************************************************************************************
+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);
+ }
+}
//**********************************************************************************************************************
projects / mothur.git / blobdiff