Exemplo n.º 1
0
//**********************************************************************************************************************
int GetSeqsCommand::readList(){
	try {
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
        map<string, string> variables; 
		variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
        variables["[extension]"] = m->getExtension(listfile);
		
		ifstream in;
		m->openInputFile(listfile, in);
		
		bool wroteSomething = false;
		int selectedCount = 0;
        
        if (m->debug) { set<string> temp; sanity["list"] = temp; }
		
		while(!in.eof()){
			
			selectedCount = 0;

			//read in list vector
			ListVector list(in);
			
			//make a new list vector
			ListVector newList;
			newList.setLabel(list.getLabel());
            
            variables["[distance]"] = list.getLabel();
            string outputFileName = getOutputFileName("list", variables);
			
			ofstream out;
			m->openOutputFile(outputFileName, out);
			outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
            
            vector<string> binLabels = list.getLabels();
            vector<string> newBinLabels;
            
            if (m->control_pressed) { in.close(); out.close();  return 0; }
			
			//for each bin
			for (int i = 0; i < list.getNumBins(); i++) {
			
				//parse out names that are in accnos file
				string binnames = list.get(i);
                vector<string> bnames;
                m->splitAtComma(binnames, bnames);
				
				string newNames = "";
                for (int j = 0; j < bnames.size(); j++) {
					string name = bnames[j];
					//if that name is in the .accnos file, add it
					if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
				}
			
				//if there are names in this bin add to new list
				if (newNames != "") { 
					newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
					newList.push_back(newNames);
                    newBinLabels.push_back(binLabels[i]);
				}
			}
				
			//print new listvector
			if (newList.getNumBins() != 0) {
				wroteSomething = true;
				newList.setLabels(newBinLabels);
                newList.printHeaders(out);
				newList.print(out);
			}
			
			m->gobble(in);
            out.close();
		}
		in.close();	
		
		
		if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
		
		m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
		
		return 0;

	}
	catch(exception& e) {
		m->errorOut(e, "GetSeqsCommand", "readList");
		exit(1);
	}
}
Exemplo n.º 2
0
//**********************************************************************************************************************
int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream& out, ofstream& outGroup, bool& wroteSomething){
	try {
		
		//make a new list vector
		ListVector newList;
		newList.setLabel(list->getLabel());
		
		int numOtus = 0;
		//for each bin
        vector<string> binLabels = list->getLabels();
        vector<string> newBinLabels;
		for (int i = 0; i < list->getNumBins(); i++) {
			if (m->control_pressed) { return 0; }
			
			//parse out names that are in accnos file
			string binnames = list->get(i);
			
			bool keepBin = false;
			string groupFileOutput = "";
			
			//parse names
			string individual = "";
			int length = binnames.length();
			for(int j=0;j<length;j++){
				if(binnames[j] == ','){
					string group = groupMap->getGroup(individual);
					if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
					
					if (m->inUsersGroups(group, Groups)) {  keepBin = true; }
					groupFileOutput += individual + "\t" + group + "\n";
					individual = "";	
					
				}
				else{  individual += binnames[j];  }
			}
			
			string group = groupMap->getGroup(individual);
			if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
			
			if (m->inUsersGroups(group, Groups)) {  keepBin = true; }
			groupFileOutput += individual + "\t" + group + "\n";
			
			//if there are sequences from the groups we want in this bin add to new list, output to groupfile
			if (keepBin) {  
				newList.push_back(binnames);
                newBinLabels.push_back(binLabels[i]);
				outGroup << groupFileOutput;
				numOtus++;
			}
		}
		
		//print new listvector
		if (newList.getNumBins() != 0) {
			wroteSomething = true;
			newList.setLabels(newBinLabels);
            newList.printHeaders(out);
            newList.print(out);
		}
		
		m->mothurOut(newList.getLabel() + " - selected " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
	
		return 0;
	}
	catch(exception& e) {
		m->errorOut(e, "GetOtusCommand", "processList");
		exit(1);
	}
}
Exemplo n.º 3
0
//**********************************************************************************************************************
int RemoveGroupsCommand::readList(){
	try {
		string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
		map<string, string> variables; 
        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
        variables["[extension]"] = m->getExtension(listfile);
				
		ifstream in;
		m->openInputFile(listfile, in);
		
		bool wroteSomething = false;
		int removedCount = 0;
		
		while(!in.eof()){
			
			removedCount = 0;
			
			//read in list vector
			ListVector list(in);
            
            variables["[tag]"] = list.getLabel();
            string outputFileName = getOutputFileName("list", variables);
			
			ofstream out;
			m->openOutputFile(outputFileName, out);
			outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
            
            vector<string> binLabels = list.getLabels();
            vector<string> newBinLabels;
			
			//make a new list vector
			ListVector newList;
			newList.setLabel(list.getLabel());
			
			//for each bin
			for (int i = 0; i < list.getNumBins(); i++) {
				if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
				
				//parse out names that are in accnos file
				string binnames = list.get(i);
				
				string newNames = "";
				while (binnames.find_first_of(',') != -1) { 
					string name = binnames.substr(0,binnames.find_first_of(','));
					binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
					
					//if that name is in the .accnos file, add it
					if (names.count(name) == 0) {  newNames += name + ",";  }
					else {
						//if you are not in the accnos file check if you are a name that needs to be changed
						map<string, string>::iterator it = uniqueToRedundant.find(name);
						if (it != uniqueToRedundant.end()) {
							newNames += it->second + ",";
						}else { removedCount++; }
					}
				}
				
				//get last name
				if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
				else { //if you are not in the accnos file check if you are a name that needs to be changed
					map<string, string>::iterator it = uniqueToRedundant.find(binnames);
					if (it != uniqueToRedundant.end()) {
						newNames += it->second + ",";
					}else { removedCount++; }
				}
				
				//if there are names in this bin add to new list
				if (newNames != "") {  
					newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
					newList.push_back(newNames);
                    newBinLabels.push_back(binLabels[i]);
				}
			}
			
			//print new listvector
			if (newList.getNumBins() != 0) {
				wroteSomething = true;
				newList.setLabels(newBinLabels);
                newList.printHeaders(out);
				newList.print(out);
			}
			
			m->gobble(in);
            out.close();
		}
		in.close();	
		
		
		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine();  }
		m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "RemoveGroupsCommand", "readList");
		exit(1);
	}
}
Exemplo n.º 4
0
//**********************************************************************************************************************
int RemoveRareCommand::processList(){
	try {
				
		//you must provide a label because the names in the listfile need to be consistent
		string thisLabel = "";
		if (allLines) { m->mothurOut("For the listfile you must select one label, using first label in your listfile."); m->mothurOutEndLine(); }
		else if (labels.size() > 1) { m->mothurOut("For the listfile you must select one label, using " + (*labels.begin()) + "."); m->mothurOutEndLine(); thisLabel = *labels.begin(); }
		else { thisLabel = *labels.begin(); }
		
		InputData input(listfile, "list");
		ListVector* list = input.getListVector();
		
		//get first one or the one we want
		if (thisLabel != "") { 	
			//use smart distancing
			set<string> userLabels; userLabels.insert(thisLabel);
			set<string> processedLabels;
			string lastLabel = list->getLabel();
			while((list != NULL) && (userLabels.size() != 0)) {
				if(userLabels.count(list->getLabel()) == 1){
					processedLabels.insert(list->getLabel());
					userLabels.erase(list->getLabel());
					break;
				}
				
				if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
					processedLabels.insert(list->getLabel());
					userLabels.erase(list->getLabel());
					delete list;
					list = input.getListVector(lastLabel);
					break;
				}
				lastLabel = list->getLabel();
				delete list;
				list = input.getListVector();
			}
			if (userLabels.size() != 0) { 
				m->mothurOut("Your file does not include the label " + thisLabel + ". I will use " + lastLabel + ".");  m->mothurOutEndLine();
				list = input.getListVector(lastLabel); 
			}
		}
        
        string thisOutputDir = outputDir;
		if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
        map<string, string> variables;
        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
        variables["[extension]"] = m->getExtension(listfile);
        variables["[tag]"] = list->getLabel();
		string outputFileName = getOutputFileName("list", variables);
        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
        variables["[extension]"] = m->getExtension(groupfile);
		string outputGroupFileName = getOutputFileName("group", variables);
        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
        variables["[extension]"] = m->getExtension(countfile);
        string outputCountFileName = getOutputFileName("count", variables);
        
		ofstream out, outGroup;
		m->openOutputFile(outputFileName, out);
		
		bool wroteSomething = false;

		
		//if groupfile is given then use it
		GroupMap* groupMap;
        CountTable ct;
		if (groupfile != "") { 
			groupMap = new GroupMap(groupfile); groupMap->readMap(); 
			SharedUtil util;
			vector<string> namesGroups = groupMap->getNamesOfGroups();
			util.setGroups(Groups, namesGroups);
			m->openOutputFile(outputGroupFileName, outGroup);
		}else if (countfile != "") {
            ct.readTable(countfile, true, false);
            if (ct.hasGroupInfo()) {
                vector<string> namesGroups = ct.getNamesOfGroups();
                SharedUtil util;
                util.setGroups(Groups, namesGroups);
            }
        }
		
		
		if (list != NULL) {
            
            vector<string> binLabels = list->getLabels();
            vector<string> newLabels;
            
			//make a new list vector
			ListVector newList;
			newList.setLabel(list->getLabel());
			
			//for each bin
			for (int i = 0; i < list->getNumBins(); i++) {
				if (m->control_pressed) {  if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close();  m->mothurRemove(outputFileName);  return 0; }
				
				//parse out names that are in accnos file
				string binnames = list->get(i);
				vector<string> names;
				string saveBinNames = binnames;
				m->splitAtComma(binnames, names);
                int binsize = names.size();
				
				vector<string> newGroupFile;
				if (groupfile != "") {
					vector<string> newNames;
					saveBinNames = "";
					for(int k = 0; k < names.size(); k++) {
						string group = groupMap->getGroup(names[k]);
						
						if (m->inUsersGroups(group, Groups)) {
							newGroupFile.push_back(names[k] + "\t" + group); 
								
							newNames.push_back(names[k]);	
							saveBinNames += names[k] + ",";
						}
					}
					names = newNames; binsize = names.size();
					saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);
				}else if (countfile != "") {
					saveBinNames = "";
                    binsize = 0;
					for(int k = 0; k < names.size(); k++) {
                        if (ct.hasGroupInfo()) {
                            vector<string> thisSeqsGroups = ct.getGroups(names[k]);
                            
                            int thisSeqsCount = 0;
                            for (int n = 0; n < thisSeqsGroups.size(); n++) {
                                if (m->inUsersGroups(thisSeqsGroups[n], Groups)) {
                                    thisSeqsCount += ct.getGroupCount(names[k], thisSeqsGroups[n]);
                                }
                            }
                            binsize += thisSeqsCount;
                            //if you don't have any seqs from the groups the user wants, then remove you.
                            if (thisSeqsCount == 0) { newGroupFile.push_back(names[k]); }
                            else { saveBinNames += names[k] + ","; }
                        }else {
                            binsize += ct.getNumSeqs(names[k]); 
                            saveBinNames += names[k] + ",";
                        }
					}
					saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1);
                }

				if (binsize > nseqs) { //keep bin
					newList.push_back(saveBinNames);
                    newLabels.push_back(binLabels[i]);
					if (groupfile != "") {  for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; }  }
                    else if (countfile != "") { for(int k = 0; k < newGroupFile.size(); k++) {  ct.remove(newGroupFile[k]); } }  
				}else {  if (countfile != "") {  for(int k = 0; k < names.size(); k++) {  ct.remove(names[k]); } }  }
			}
			
			//print new listvector
			if (newList.getNumBins() != 0) {
				wroteSomething = true;
				newList.setLabels(newLabels);
                newList.printHeaders(out);
                newList.print(out);
			}
		}	
		
		out.close();
		if (groupfile != "") { outGroup.close(); outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); }
        if (countfile != "") { 
            if (ct.hasGroupInfo()) {
                vector<string> allGroups = ct.getNamesOfGroups();
                for (int i = 0; i < allGroups.size(); i++) {
                    if (!m->inUsersGroups(allGroups[i], Groups)) { ct.removeGroup(allGroups[i]); }
                }

            }
            ct.printTable(outputCountFileName);
            outputTypes["count"].push_back(outputCountFileName); outputNames.push_back(outputCountFileName); 
        }
		
		if (wroteSomething == false) {  m->mothurOut("Your file contains only rare sequences."); m->mothurOutEndLine();  }
		outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
		
		return 0;
	}
	catch(exception& e) {
		m->errorOut(e, "RemoveRareCommand", "processList");
		exit(1);
	}
}