//**********************************************************************************************************************
-SharedCommand::SharedCommand(){
+SharedCommand::SharedCommand(string o) : outputDir(o) {
try {
globaldata = GlobalData::getInstance();
//getting output filename
filename = globaldata->inputFileName;
- filename = getRootName(filename);
+ if (outputDir == "") { outputDir += hasPath(filename); }
+
+ filename = outputDir + getRootName(getSimpleName(filename));
filename = filename + "shared";
+
openOutputFile(filename, out);
+ pickedGroups = false;
+
+ groupMap = globaldata->gGroupmap;
+
+ //if hte user has not specified any groups then use them all
+ if (globaldata->Groups.size() == 0) {
+ groups = groupMap->namesOfGroups;
+ }else{ //they have specified groups
+ groups = globaldata->Groups;
+ pickedGroups = true;
+ }
+
+ //fill filehandles with neccessary ofstreams
+ int i;
+ ofstream* temp;
+ for (i=0; i<groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[groups[i]] = temp;
+ }
+
+ //set fileroot
+ fileroot = outputDir + getRootName(getSimpleName(globaldata->getListFile()));
+
+ //clears file before we start to write to it below
+ for (int i=0; i<groups.size(); i++) {
+ remove((fileroot + groups[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";
+ errorOut(e, "SharedCommand", "SharedCommand");
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";
- exit(1);
- }
-
}
//**********************************************************************************************************************
int SharedCommand::execute(){
try {
- globaldata = GlobalData::getInstance();
+
//lookup.clear();
- int count = 1;
string errorOff = "no error";
-
+ //errorOff = "";
+cout << globaldata->inputFileName << endl;
//read in listfile
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
+ delete read;
input = globaldata->ginput;
SharedList = globaldata->gSharedList;
- SharedListVector* lastList = SharedList;
- //lookup = SharedList->getSharedRAbundVector();
- //vector<SharedRAbundVector*> lastLookup = lookup;
+ string lastLabel = SharedList->getLabel();
+ vector<SharedRAbundVector*> lookup;
+
+ if ((globaldata->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) { //if the user has not specified any groups and their files don't match exit with error
+ 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 user has specified groups make new groupfile for them
+ if (globaldata->Groups.size() != 0) { //make new group file
+ string groups = "";
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ groups += globaldata->Groups[i] + ".";
+ }
+
+ string newGroupFile = getRootName(globaldata->inputFileName) + groups + "groups";
+ ofstream outGroups;
+ openOutputFile(newGroupFile, outGroups);
+
+ vector<string> names = groupMap->getNamesSeqs();
+ string groupName;
+ for (int i = 0; i < names.size(); i++) {
+ groupName = groupMap->getGroup(names[i]);
+ if (isValidGroup(groupName, globaldata->Groups)) {
+ outGroups << names[i] << '\t' << groupName << endl;
+ }
+ }
+ outGroups.close();
+ }
//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;
-
- shared = new Shared();
+ set<string> userLabels = globaldata->labels;
+
+ while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
- while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
-
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+ lookup = SharedList->getSharedRAbundVector();
+ if (pickedGroups) { //check for otus with no seqs in them
+ eliminateZeroOTUS(lookup);
+ }
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
- shared->getSharedVectors(SharedList); //fills sharedGroups with new info and updates sharedVector
- printSharedData(); //prints info to the .shared file
+ 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(lastList->getLabel()) != 1)) {
- shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
- printSharedData(); //prints info to the .shared file
-
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ 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();
+ if (pickedGroups) { //check for otus with no seqs in them
+ eliminateZeroOTUS(lookup);
+ }
+ 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);
}
- if (count != 1) { delete lastList; }
- lastList = SharedList;
+
+ lastLabel = SharedList->getLabel();
+
+ delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
-
- //if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- //lastLookup = lookup;
- //if (SharedList != NULL) { lookup = SharedList->getSharedRAbundVector(); }
}
//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(lastList->getLabel()) != 1) {
- //cout << ". I will use " << lastList->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
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) {
- shared->getSharedVectors(lastList); //fills sharedGroups with new info and updates sharedVector
- printSharedData(); //prints info to the .shared file
+ if (SharedList != NULL) { delete SharedList; }
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
+ if (pickedGroups) { //check for otus with no seqs in them
+ eliminateZeroOTUS(lookup);
+ }
+ 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;
}
- delete lastList;
- delete shared;
+ globaldata->gSharedList = NULL;
+
out.close();
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
+ }
+
+ globaldata->setSharedFile(filename);
+
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";
+}
+//**********************************************************************************************************************
+void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
+ try {
+
+ //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) {
+ errorOut(e, "SharedCommand", "printSharedData");
exit(1);
}
-
}
//**********************************************************************************************************************
-void SharedCommand::printSharedData() {
+void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
try {
-
- ///for (int i = 0; i < thislookup.size(); i++) {
- // out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
-//cout << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
- // thislookup[i]->print(out);
- // }
- //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
+
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
}
+
+ //for each bin
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ }
+ //else{ cout << "bin # " << i << " is all zeros" << endl; }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+ thislookup = newLookup;
+
+
}
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", "eliminateZeroOTUS");
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);
}
-
}
//**********************************************************************************************************************
SharedCommand::~SharedCommand(){
//delete list;
- delete read;
+
}
//**********************************************************************************************************************
+
+bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
+ try {
+ for (int i = 0; i < groups.size(); i++) {
+ if (groupname == groups[i]) { return true; }
+ }
+
+ return false;
+ }
+ catch(exception& e) {
+ errorOut(e, "SharedCommand", "isValidGroup");
+ exit(1);
+ }
+}
+/************************************************************/
+
+
projects / mothur.git / blobdiff