int SensSpecCommand::processColumn(){ try{ string origCutoff = ""; bool getCutoff = 0; if(cutoff == -1.00) { getCutoff = 1; } else { origCutoff = toString(cutoff); cutoff += (0.49 / double(precision)); } set<string> seqPairSet; int numSeqs = 0; InputData input(listFile, "list"); ListVector* list = input.getListVector(); 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 = labels; while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; return 0; } if(allLines == 1 || labels.count(list->getLabel()) == 1){ processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); //process numSeqs = fillSeqPairSet(seqPairSet, list); process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs); } if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); delete list; list = input.getListVector(lastLabel); processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); //process numSeqs = fillSeqPairSet(seqPairSet, list); process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs); //restore real lastlabel to save below list->setLabel(saveLabel); } lastLabel = list->getLabel(); delete list; list = input.getListVector(); } //output error messages about any remaining user labels set<string>::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } //run last label if you need to if (needToRun == true) { if (list != NULL) { delete list; } list = input.getListVector(lastLabel); //process numSeqs = fillSeqPairSet(seqPairSet, list); delete list; process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs); } return 0; } catch(exception& e) { m->errorOut(e, "SensSpecCommand", "processColumn"); exit(1); } }
int GetSharedOTUCommand::execute(){ try { if (abort == true) { if (calledHelp) { return 0; } return 2; } if ( sharedfile != "") { runShared(); } else { m->setGroups(Groups); groupMap = new GroupMap(groupfile); int error = groupMap->readMap(); if (error == 1) { delete groupMap; return 0; } if (m->control_pressed) { delete groupMap; return 0; } if (Groups.size() == 0) { Groups = groupMap->getNamesOfGroups(); //make string for outputfile name userGroups = "unique."; for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; } userGroups = userGroups.substr(0, userGroups.length()-1); }else{ //sanity check for group names SharedUtil util; vector<string> namesOfGroups = groupMap->getNamesOfGroups(); util.setGroups(Groups, namesOfGroups); groupMap->setNamesOfGroups(namesOfGroups); } //put groups in map to find easier for(int i = 0; i < Groups.size(); i++) { groupFinder[Groups[i]] = Groups[i]; } if (fastafile != "") { ifstream inFasta; m->openInputFile(fastafile, inFasta); while(!inFasta.eof()) { if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; } Sequence seq(inFasta); m->gobble(inFasta); if (seq.getName() != "") { seqs.push_back(seq); } } inFasta.close(); } ListVector* lastlist = NULL; string lastLabel = ""; //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 = labels; ifstream in; m->openInputFile(listfile, in); //as long as you are not at the end of the file or done wih the lines you want while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) { if (m->control_pressed) { if (lastlist != NULL) { delete lastlist; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); delete groupMap; return 0; } list = new ListVector(in); if(allLines == 1 || labels.count(list->getLabel()) == 1){ m->mothurOut(list->getLabel()); process(list); processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); } if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); m->mothurOut(lastlist->getLabel()); process(lastlist); processedLabels.insert(lastlist->getLabel()); userLabels.erase(lastlist->getLabel()); //restore real lastlabel to save below list->setLabel(saveLabel); } lastLabel = list->getLabel(); if (lastlist != NULL) { delete lastlist; } lastlist = list; } in.close(); //output error messages about any remaining user labels set<string>::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } //run last label if you need to if (needToRun == true) { m->mothurOut(lastlist->getLabel()); process(lastlist); processedLabels.insert(lastlist->getLabel()); userLabels.erase(lastlist->getLabel()); } //reset groups parameter m->clearGroups(); if (lastlist != NULL) { delete lastlist; } if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; } } //set fasta file as new current fastafile string current = ""; itTypes = outputTypes.find("fasta"); if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } } if (output == "accnos") { itTypes = outputTypes.find("accnos"); if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); } } } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); return 0; } catch(exception& e) { m->errorOut(e, "GetSharedOTUCommand", "execute"); exit(1); } }
//********************************************************************************************************************** //returns a vector of listVectors where "little" vector is first vector<ListVector> OtuHierarchyCommand::getListVectors() { try { int pos; //to use in smart distancing, position of last read in file int lastPos; vector<ListVector> lists; //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 = labels; //open file ifstream in; m->openInputFile(listFile, in); //get first list vector in file ListVector* list = NULL; string lastLabel = ""; if (!in.eof()) { pos = in.tellg(); lastPos = pos; list = new ListVector(in); m->gobble(in); lastLabel = list->getLabel(); } while ((list != NULL) && (userLabels.size() != 0)) { if (m->control_pressed) { in.close(); delete list; return lists; } //is this a listvector that we want? if(labels.count(list->getLabel()) == 1){ //make copy of listvector ListVector temp(*list); lists.push_back(temp); processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); } //you have a label the user want that is smaller than this label and the last label has not already been processed if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); int savePos = in.tellg(); //get smart distance line delete list; in.seekg(lastPos); if (!in.eof()) { list = new ListVector(in); }else { list = NULL; } //make copy of listvector ListVector temp(*list); lists.push_back(temp); processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); //restore real lastlabel to save below list->setLabel(saveLabel); in.seekg(savePos); } lastLabel = list->getLabel(); lastPos = pos; //get next line delete list; if (!in.eof()) { pos = in.tellg(); list = new ListVector(in); m->gobble(in); }else { list = NULL; } } if (m->control_pressed) { in.close(); return lists; } //output error messages about any remaining user labels set<string>::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } if (m->control_pressed) { in.close(); return lists; } //run last label if you need to if (needToRun == true) { if (list != NULL) { delete list; } in.seekg(lastPos); if (!in.eof()) { list = new ListVector(in); //make copy of listvector ListVector temp(*list); lists.push_back(temp); delete list; } } in.close(); return lists; } catch(exception& e) { m->errorOut(e, "OtuHierarchyCommand", "getListVectors"); exit(1); } }
//********************************************************************************************************************** int GetRAbundCommand::processList(ofstream& out){ try { CountTable ct; ct.readTable(countfile, false, false); InputData input(inputfile, format); ListVector* list = input.getListVector(); 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 = labels; if (m->control_pressed) { delete list; return 0; } while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { if(allLines == 1 || labels.count(list->getLabel()) == 1){ m->mothurOut(list->getLabel()); m->mothurOutEndLine(); if (m->control_pressed) { delete list; return 0; } RAbundVector* rabund = new RAbundVector(); createRabund(ct, list, rabund); if(sorted) { rabund->print(out); } else { rabund->nonSortedPrint(out); } delete rabund; processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); } if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); delete list; list = input.getListVector(lastLabel); m->mothurOut(list->getLabel()); m->mothurOutEndLine(); if (m->control_pressed) { delete list; return 0; } RAbundVector* rabund = new RAbundVector(); createRabund(ct, list, rabund); if(sorted) { rabund->print(out); } else { rabund->nonSortedPrint(out); } delete rabund; processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); //restore real lastlabel to save below list->setLabel(saveLabel); } lastLabel = list->getLabel(); delete list; list = input.getListVector(); } //output error messages about any remaining user labels set<string>::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } //run last label if you need to if (needToRun == true) { if (list != NULL) { delete list; } list = input.getListVector(lastLabel); m->mothurOut(list->getLabel()); m->mothurOutEndLine(); if (m->control_pressed) { delete list; return 0; } RAbundVector* rabund = new RAbundVector(); createRabund(ct, list, rabund); if(sorted) { rabund->print(out); } else { rabund->nonSortedPrint(out); } delete rabund; delete list; } return 0; } catch(exception& e) { m->errorOut(e, "GetRAbundCommand", "processList"); exit(1); } }
//********************************************************************************************************************** int RemoveRareCommand::processList(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile); string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); ofstream out, outGroup; m->openOutputFile(outputFileName, out); bool wroteSomething = false; //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); } } //if groupfile is given then use it GroupMap* groupMap; if (groupfile != "") { groupMap = new GroupMap(groupfile); groupMap->readMap(); SharedUtil util; vector<string> namesGroups = groupMap->getNamesOfGroups(); util.setGroups(Groups, namesGroups); m->openOutputFile(outputGroupFileName, outGroup); } if (list != NULL) { //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); 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; saveBinNames = saveBinNames.substr(0, saveBinNames.length()-1); } if (names.size() > nseqs) { //keep bin newList.push_back(saveBinNames); for(int k = 0; k < newGroupFile.size(); k++) { outGroup << newGroupFile[k] << endl; } } } //print new listvector if (newList.getNumBins() != 0) { wroteSomething = true; newList.print(out); } } out.close(); if (groupfile != "") { outGroup.close(); outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); } 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); } }
//********************************************************************************************************************** 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); } }
//********************************************************************************************************************** int GetOtusCommand::readListGroup(){ try { InputData* input = new InputData(listfile, "list"); ListVector* list = input->getListVector(); string lastLabel = list->getLabel(); //using first label seen if none is provided if (label == "") { label = lastLabel; } string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } map<string, string> variables; variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile)); variables["[tag]"] = label; variables["[extension]"] = m->getExtension(listfile); string outputFileName = getOutputFileName("list", variables); ofstream out; m->openOutputFile(outputFileName, out); string GroupOutputDir = outputDir; if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); } variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)); variables["[extension]"] = m->getExtension(groupfile); string outputGroupFileName = getOutputFileName("group", variables); ofstream outGroup; m->openOutputFile(outputGroupFileName, outGroup); //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set<string> labels; labels.insert(label); set<string> processedLabels; set<string> userLabels = labels; bool wroteSomething = false; //as long as you are not at the end of the file or done wih the lines you want while((list != NULL) && (userLabels.size() != 0)) { if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);return 0; } if(labels.count(list->getLabel()) == 1){ processList(list, groupMap, out, outGroup, wroteSomething); processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); } if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); delete list; list = input->getListVector(lastLabel); processList(list, groupMap, out, outGroup, wroteSomething); processedLabels.insert(list->getLabel()); userLabels.erase(list->getLabel()); //restore real lastlabel to save below list->setLabel(saveLabel); } lastLabel = list->getLabel(); delete list; list = NULL; //get next line to process list = input->getListVector(); } if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); return 0; } //output error messages about any remaining user labels set<string>::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } //run last label if you need to if (needToRun == true) { if (list != NULL) { delete list; } list = input->getListVector(lastLabel); processList(list, groupMap, out, outGroup, wroteSomething); delete list; list = NULL; } out.close(); outGroup.close(); if (wroteSomething == false) { m->mothurOut("At distance " + label + " your file does NOT contain any otus containing sequences from the groups you wish to get."); m->mothurOutEndLine(); } outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName); return 0; } catch(exception& e) { m->errorOut(e, "GetOtusCommand", "readList"); exit(1); } }