EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) { try { data.clear(); //clear out old values CountTable* ct = t->getCountTable(); if (m->control_pressed) { return data; } //initialize weighted score WScore[(groupA+groupB)] = 0.0; double D = 0.0; set<int> validBranches; vector<string> groups; groups.push_back(groupA); groups.push_back(groupB); //adding the wieghted sums from group i for (int j = 0; j < t->groupNodeInfo[groups[0]].size(); j++) { //the leaf nodes that have seqs from group i map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[0]][j]].pcount.find(groups[0]); int numSeqsInGroupI = it->second; double sum = getLengthToRoot(t, t->groupNodeInfo[groups[0]][j], groups[0], groups[1]); double weightedSum = ((numSeqsInGroupI * sum) / (double)ct->getGroupCount(groups[0])); D += weightedSum; } //adding the wieghted sums from group l for (int j = 0; j < t->groupNodeInfo[groups[1]].size(); j++) { //the leaf nodes that have seqs from group l map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[1]][j]].pcount.find(groups[1]); int numSeqsInGroupL = it->second; double sum = getLengthToRoot(t, t->groupNodeInfo[groups[1]][j], groups[0], groups[1]); double weightedSum = ((numSeqsInGroupL * sum) / (double)ct->getGroupCount(groups[1])); D += weightedSum; } //calculate u for the group comb for(int i=0;i<t->getNumNodes();i++){ if (m->control_pressed) { return data; } double u; //int pcountSize = 0; //does this node have descendants from groupA it = t->tree[i].pcount.find(groupA); //if it does u = # of its descendants with a certain group / total number in tree with a certain group if (it != t->tree[i].pcount.end()) { u = (double) t->tree[i].pcount[groupA] / (double) ct->getGroupCount(groupA); }else { u = 0.00; } //does this node have descendants from group l it = t->tree[i].pcount.find(groupB); //if it does subtract their percentage from u if (it != t->tree[i].pcount.end()) { u -= (double) t->tree[i].pcount[groupB] / (double) ct->getGroupCount(groupB); } if (includeRoot) { if (t->tree[i].getBranchLength() != -1) { u = abs(u * t->tree[i].getBranchLength()); WScore[(groupA+groupB)] += u; } }else{ //if this is not the root then add it if (rootForGrouping[groups].count(i) == 0) { if (t->tree[i].getBranchLength() != -1) { u = abs(u * t->tree[i].getBranchLength()); WScore[(groupA+groupB)] += u; } } } } /********************************************************/ //calculate weighted score for the group combination double UN; UN = (WScore[(groupA+groupB)] / D); if (isnan(UN) || isinf(UN)) { UN = 0; } data.push_back(UN); return data; } catch(exception& e) { m->errorOut(e, "Weighted", "getValues"); exit(1); } }
//********************************************************************************************************************** int SplitGroupCommand::runCount(){ try { CountTable ct; ct.readTable(countfile, true, false); if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, cannot split by group.\n"); m->control_pressed = true; } if (m->control_pressed) { return 0; } vector<string> namesGroups = ct.getNamesOfGroups(); SharedUtil util; util.setGroups(Groups, namesGroups); //fill filehandles with neccessary ofstreams map<string, string> ffiles; //group -> filename map<string, string> cfiles; //group -> filename for (int i=0; i<Groups.size(); i++) { ofstream ftemp, ctemp; map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile)); variables["[group]"] = Groups[i]; string newFasta = getOutputFileName("fasta",variables); outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta); ffiles[Groups[i]] = newFasta; m->openOutputFile(newFasta, ftemp); ftemp.close(); variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile)); string newCount = getOutputFileName("count",variables); outputNames.push_back(newCount); outputTypes["count"].push_back(newCount); cfiles[Groups[i]] = newCount; m->openOutputFile(newCount, ctemp); ctemp << "Representative_Sequence\ttotal\t" << Groups[i] << endl; ctemp.close(); } ifstream in; m->openInputFile(fastafile, in); while (!in.eof()) { Sequence seq(in); m->gobble(in); if (m->control_pressed) { break; } if (seq.getName() != "") { vector<string> thisSeqsGroups = ct.getGroups(seq.getName()); for (int i = 0; i < thisSeqsGroups.size(); i++) { if (m->inUsersGroups(thisSeqsGroups[i], Groups)) { //if this sequence belongs to a group we want them print ofstream outf, outc; m->openOutputFileAppend(ffiles[thisSeqsGroups[i]], outf); seq.printSequence(outf); outf.close(); int numSeqs = ct.getGroupCount(seq.getName(), thisSeqsGroups[i]); m->openOutputFileAppend(cfiles[thisSeqsGroups[i]], outc); outc << seq.getName() << '\t' << numSeqs << '\t' << numSeqs << endl; outc.close(); } } } } in.close(); return 0; } catch(exception& e) { m->errorOut(e, "SplitGroupCommand", "runCount"); exit(1); } }
//********************************************************************************************************************** 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); } }