globaldata = GlobalData::getInstance();
//read in group map info.
- groupMap = new GroupMap(globaldata->getGroupFile());
- groupMap->readMap();
-
+ //groupMap = new GroupMap(globaldata->getGroupFile());
+ //groupMap->readMap();
+ groupMap = globaldata->gGroupmap;
+
//fill filehandles with neccessary ofstreams
int i;
ofstream* temp;
+ SharedListVector* templist;
for (i=0; i<groupMap->getNumGroups(); i++) {
temp = new ofstream;
+ templist = new SharedListVector();
filehandles[groupMap->namesOfGroups[i]] = temp;
+ mapOfLists[groupMap->namesOfGroups[i]] = templist;
}
//set fileroot
fileroot = getRootName(globaldata->getListFile());
- //open output list files
- for (i=0; i<groupMap->getNumGroups(); i++) {//opens an output file for each group
- openOutputFile(fileroot + groupMap->namesOfGroups[i] + ".list", *(filehandles[groupMap->namesOfGroups[i]]));
+ //clears file before we start to write to it below
+ for (int i=0; i<groupMap->getNumGroups(); i++) {
+ remove((fileroot + groupMap->namesOfGroups[i] + ".list").c_str());
}
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParseListCommand class Function ParseListCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParseListCommand class function ParseListCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ParseListCommand", "ParseListCommand");
exit(1);
}
+
}
/***********************************************************************/
-void ParseListCommand::parse(int index) {
+void ParseListCommand::parse(int index, SharedListVector* list) {
try {
- string prefix, suffix, groupsName;
- suffix = list->get(index);
-
- while (suffix.find_first_of(',') != -1) {//while you still have sequences
- prefix = suffix.substr(0,suffix.find_first_of(','));
- if ((suffix.find_first_of(',')+1) <= suffix.length()) { //checks to make sure you don't have comma at end of string
- suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
+ string member, bin, groupName;
+ bin = list->get(index);
+
+ while (bin.find_first_of(',') != -1) {//while you still have sequences
+ member = bin.substr(0,bin.find_first_of(','));
+ if ((bin.find_first_of(',')+1) <= bin.length()) { //checks to make sure you don't have comma at end of string
+ bin = bin.substr(bin.find_first_of(',')+1, bin.length());
}
- groupsName = groupMap->getGroup(prefix);
- if (groupsName != "not found") {
- listGroups[groupsName] = listGroups[groupsName] + "," + prefix; //adds prefix to the correct group.
+ groupName = groupMap->getGroup(member);
+ if (groupName != "not found") {
+ listGroups[groupName] = listGroups[groupName] + "," + member; //adds prefix to the correct group.
}else {
- cerr << "Error: Sequence '" << prefix << "' was not found in the group file, please correct\n";
+ mothurOut("Error: Sequence '" + toString(member) + "' was not found in the group file, please correct\n");
}
}
//save last name after comma
- groupsName = groupMap->getGroup(suffix);
- if (groupsName != "not found") {
- listGroups[groupsName] = listGroups[groupsName] + "," + suffix; //adds prefix to the correct group.
+ groupName = groupMap->getGroup(bin);
+ if (groupName != "not found") {
+ listGroups[groupName] = listGroups[groupName] + "," + bin; //adds prefix to the correct group.
}else {
- cerr << "Error: Sequence '" << suffix << "' was not found in the group file, please correct\n";
+ mothurOut("Error: Sequence '" + toString(bin) + "' was not found in the group file, please correct\n");
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParseListCommand class Function parse. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParseListCommand class function parse. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ParseListCommand", "parse");
exit(1);
}
}
int ParseListCommand::execute(){
try{
- globaldata = GlobalData::getInstance();
+
+ int count = 1;
//read in listfile
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
input = globaldata->ginput;
list = globaldata->gSharedList;
-
- //read in group map info.
- groupMap = new GroupMap(globaldata->getGroupFile());
- groupMap->readMap();
-
- string seq, label;
- int i;
- //create new list vectors to fill with parsed data
- for (i=0; i<groupMap->getNumGroups(); i++) {
- groupOfLists[groupMap->namesOfGroups[i]] = new SharedListVector();
- }
-
+ string lastLabel = list->getLabel();
+
+ //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;
+
//parses and sets each groups listvector
- while(list != NULL){
- label = list->getLabel();
- for(i=0; i<list->size(); i++) {
- parse(i); //parses data[i] list of sequence names
- for (it=listGroups.begin(); it != listGroups.end(); it++) { //loop through map and set new list vectors
- seq = it->second;
- seq = seq.substr(1, seq.length()); //rips off extra comma
- groupOfLists[it->first]->push_back(seq); //sets new listvector for each group
- }
- listGroups.clear();
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lastLabel) == 1){
+ mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ userLines.erase(count);
}
- //prints each new list file
- for (i=0; i<groupMap->getNumGroups(); i++) {
- groupOfLists[groupMap->namesOfGroups[i]]->setLabel(label);
- groupOfLists[groupMap->namesOfGroups[i]]->print(*(filehandles[groupMap->namesOfGroups[i]]));
- groupOfLists[groupMap->namesOfGroups[i]]->clear();
+
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete list;
+ list = input->getSharedListVector(lastLabel);
+
+ mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
}
+
+
+ lastLabel = list->getLabel();
+
+ delete list;
list = input->getSharedListVector();
+ count++;
}
- //set groupmap for .shared commands
- globaldata->gGroupmap = groupMap;
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ needToRun = true;
+ }else {
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ delete list;
+ list = input->getSharedListVector(lastLabel);
+
+ mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(list);
+ delete list;
+ }
+
+ globaldata->gSharedList = NULL;
+ //delete list vectors to fill with parsed data
+ for (it2 = mapOfLists.begin(); it2 != mapOfLists.end(); it2++) {
+ delete it2->second;
+ }
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it2->second;
+ }
+
+ delete input; globaldata->ginput = NULL;
+ delete read;
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParseListCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ParseListCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ParseListCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//**********************************************************************************************************************
ParseListCommand::~ParseListCommand(){
- delete list;
- delete input;
- delete read;
+
+
}
//**********************************************************************************************************************
+void ParseListCommand::process(SharedListVector* thisList) {
+ try {
+ string seq;
+
+ for(int i=0; i<thisList->size(); i++) {
+ parse(i, thisList); //parses data[i] list of sequence names
+ for (it=listGroups.begin(); it != listGroups.end(); it++) { //loop through map and set new list vectors
+ seq = it->second;
+ seq = seq.substr(1, seq.length()); //rips off extra comma
+ mapOfLists[it->first]->push_back(seq); //sets new listvector for each group
+ }
+ listGroups.clear();
+ }
+ //prints each new list file
+ for (int i=0; i<groupMap->getNumGroups(); i++) {
+ openOutputFileAppend(fileroot + groupMap->namesOfGroups[i] + ".list", *(filehandles[groupMap->namesOfGroups[i]]));
+ mapOfLists[groupMap->namesOfGroups[i]]->setLabel(thisList->getLabel());
+ mapOfLists[groupMap->namesOfGroups[i]]->print(*(filehandles[groupMap->namesOfGroups[i]]));
+ mapOfLists[groupMap->namesOfGroups[i]]->clear();
+ (*(filehandles[groupMap->namesOfGroups[i]])).close();
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "ParseListCommand", "process");
+ exit(1);
+ }
+}
projects / mothur.git / blobdiff