X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=treegroupscommand.cpp;h=80698f1b4b0317719421dbe9c4af3c0583bd9d97;hp=c26199d673088b5b64872b672ab8e64ca780e616;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=85115bc28619f27bdeffd85a8a14d52bab958f5f diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp index c26199d..80698f1 100644 --- a/treegroupscommand.cpp +++ b/treegroupscommand.cpp @@ -14,22 +14,23 @@ //********************************************************************************************************************** vector TreeGroupCommand::setParameters(){ try { - CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared); - CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname); - CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn); - CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); - CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample); - CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff); - CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc); + CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false,true); parameters.push_back(pshared); + CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false); parameters.push_back(pphylip); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn","",false,false); parameters.push_back(pcount); + CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn","tree",false,false); parameters.push_back(pcolumn); + CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters); + CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample); + CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff); + CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); //CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -70,6 +71,21 @@ string TreeGroupCommand::getHelpString(){ } } //********************************************************************************************************************** +string TreeGroupCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "tree") { pattern = "[filename],[calc],[distance],[tag],tre-[filename],tre"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** TreeGroupCommand::TreeGroupCommand(){ try { abort = true; calledHelp = true; @@ -140,6 +156,14 @@ TreeGroupCommand::TreeGroupCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } + + it = parameters.find("count"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["count"] = inputDir + it->second; } + } } //check for required parameters @@ -162,6 +186,11 @@ TreeGroupCommand::TreeGroupCommand(string option) { if (namefile == "not open") { abort = true; } else if (namefile == "not found") { namefile = ""; } else { m->setNameFile(namefile); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { abort = true; countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) { //is there are current file available for either of these? @@ -184,15 +213,20 @@ TreeGroupCommand::TreeGroupCommand(string option) { else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; } if (columnfile != "") { - if (namefile == "") { + if ((namefile == "") && (countfile == "")){ namefile = m->getNameFile(); if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); } else { - m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); - abort = true; + countfile = m->getCountTableFile(); + if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You need to provide a namefile or countfile if you are going to use the column format."); m->mothurOutEndLine(); + abort = true; + } } } } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... @@ -266,8 +300,8 @@ TreeGroupCommand::TreeGroupCommand(string option) { TreeGroupCommand::~TreeGroupCommand(){ if (abort == false) { if (format == "sharedfile") { delete input; } - else { delete readMatrix; delete matrix; delete list; } - delete tmap; + else { delete list; } + delete ct; } } @@ -380,14 +414,25 @@ int TreeGroupCommand::execute(){ m->runParse = false; //create treemap class from groupmap for tree class to use - tmap = new TreeMap(); - tmap->makeSim(m->getAllGroups()); + ct = new CountTable(); + set nameMap; + map groupMap; + set gps; + for (int i = 0; i < m->getAllGroups().size(); i++) { + nameMap.insert(m->getAllGroups()[i]); + gps.insert(m->getAllGroups()[i]); + groupMap[m->getAllGroups()[i]] = m->getAllGroups()[i]; + } + ct->createTable(nameMap, groupMap, gps); //clear globaldatas old tree names if any m->Treenames.clear(); //fills globaldatas tree names - m->Treenames = m->getGroups(); + //m->Treenames = m->getGroups(); + for (int k = 0; k < lookup.size(); k++) { + m->Treenames.push_back(lookup[k]->getGroup()); + } if (m->control_pressed) { return 0; } @@ -398,51 +443,66 @@ int TreeGroupCommand::execute(){ }else{ //read in dist file filename = inputfile; - + + ReadMatrix* readMatrix; if (format == "column") { readMatrix = new ReadColumnMatrix(filename); } else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); } readMatrix->setCutoff(cutoff); - if(namefile != ""){ - nameMap = new NameAssignment(namefile); - nameMap->readMap(); - } - else{ - nameMap = NULL; - } - - readMatrix->read(nameMap); - list = readMatrix->getListVector(); - matrix = readMatrix->getMatrix(); + ct = NULL; + nameMap = NULL; + if(namefile != ""){ + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + readMatrix->read(nameMap); + }else if (countfile != "") { + ct = new CountTable(); + ct->readTable(countfile, true); + readMatrix->read(ct); + }else { + readMatrix->read(nameMap); + } + list = readMatrix->getListVector(); + SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix(); + + //clear globaldatas old tree names if any + m->Treenames.clear(); + //make treemap - tmap = new TreeMap(); - - if (m->control_pressed) { return 0; } - - tmap->makeSim(list); + if (ct != NULL) { delete ct; } + ct = new CountTable(); + set nameMap; + map groupMap; + set gps; + for (int i = 0; i < list->getNumBins(); i++) { + string bin = list->get(i); + nameMap.insert(bin); + gps.insert(bin); + groupMap[bin] = bin; + m->Treenames.push_back(bin); + } + ct->createTable(nameMap, groupMap, gps); - vector namesGroups = tmap->getNamesOfGroups(); + vector namesGroups = ct->getNamesOfGroups(); m->setGroups(namesGroups); - - //clear globaldatas old tree names if any - m->Treenames.clear(); - - //fills globaldatas tree names - m->Treenames = m->getGroups(); //used in tree constructor m->runParse = false; if (m->control_pressed) { return 0; } - vector< vector > matrix = makeSimsDist(); + vector< vector > matrix = makeSimsDist(dMatrix); + delete readMatrix; + delete dMatrix; if (m->control_pressed) { return 0; } //create a new filename - string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "tre"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile)); + string outputFile = getOutputFileName("tree",variables); outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); Tree* newTree = createTree(matrix); @@ -482,13 +542,12 @@ int TreeGroupCommand::execute(){ Tree* TreeGroupCommand::createTree(vector< vector >& simMatrix){ try { //create tree - t = new Tree(tmap, simMatrix); + t = new Tree(ct, simMatrix); if (m->control_pressed) { delete t; t = NULL; return t; } //assemble tree - map empty; - t->assembleTree(empty); + t->assembleTree(); return t; } @@ -534,7 +593,7 @@ void TreeGroupCommand::printSims(ostream& out, vector< vector >& simMatr } } /***********************************************************/ -vector< vector > TreeGroupCommand::makeSimsDist() { +vector< vector > TreeGroupCommand::makeSimsDist(SparseDistanceMatrix* matrix) { try { numGroups = list->size(); @@ -549,13 +608,17 @@ vector< vector > TreeGroupCommand::makeSimsDist() { //go through sparse matrix and fill sims //go through each cell in the sparsematrix - for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){ - //similairity = -(distance-1) - simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0); - simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0); - - if (m->control_pressed) { return simMatrix; } + for (int i = 0; i < matrix->seqVec.size(); i++) { + for (int j = 0; j < matrix->seqVec[i].size(); j++) { + + //already checked everyone else in row + if (i < matrix->seqVec[i][j].index) { + simMatrix[i][matrix->seqVec[i][j].index] = -(matrix->seqVec[i][j].dist -1.0); + simMatrix[matrix->seqVec[i][j].index][i] = -(matrix->seqVec[i][j].dist -1.0); + if (m->control_pressed) { return simMatrix; } + } + } } return simMatrix; @@ -581,6 +644,7 @@ int TreeGroupCommand::makeSimsShared() { }else { m->clearGroups(); Groups.clear(); + m->Treenames.clear(); vector temp; for (int i = 0; i < lookup.size(); i++) { if (lookup[i]->getNumSeqs() < subsampleSize) { @@ -589,6 +653,7 @@ int TreeGroupCommand::makeSimsShared() { }else { Groups.push_back(lookup[i]->getGroup()); temp.push_back(lookup[i]); + m->Treenames.push_back(lookup[i]->getGroup()); } } lookup = temp; @@ -597,8 +662,18 @@ int TreeGroupCommand::makeSimsShared() { if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; } } - numGroups = lookup.size(); + + //sanity check to make sure processors < numComparisions + int numDists = 0; + for(int i=0;i processors) { break; } + } + } + if (numDists < processors) { processors = numDists; } + lines.resize(processors); for (int i = 0; i < processors; i++) { lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups); @@ -827,6 +902,9 @@ int TreeGroupCommand::process(vector thisLookup) { //Close all thread handles and free memory allocations. for(int i=0; i < pDataArray.size(); i++){ + if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; + } for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; } for (int k = 0; k < calcDists.size(); k++) { @@ -850,35 +928,17 @@ int TreeGroupCommand::process(vector thisLookup) { thisItersLookup.clear(); for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); } } + + if (m->debug) { m->mothurOut("[DEBUG]: iter = " + toString(thisIter) + ".\n"); } } - + + if (m->debug) { m->mothurOut("[DEBUG]: done with iters.\n"); } + if (iters != 1) { //we need to find the average distance and standard deviation for each groups distance + vector< vector > calcAverages = m->getAverages(calcDistsTotals); - vector< vector > calcAverages; calcAverages.resize(treeCalculators.size()); - for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero. - calcAverages[i].resize(calcDistsTotals[0][i].size()); - - for (int j = 0; j < calcAverages[i].size(); j++) { - calcAverages[i][j].seq1 = calcDists[i][j].seq1; - calcAverages[i][j].seq2 = calcDists[i][j].seq2; - calcAverages[i][j].dist = 0.0; - } - } - - for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator - for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero. - for (int j = 0; j < calcAverages[i].size(); j++) { - calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist; - } - } - } - - for (int i = 0; i < calcAverages.size(); i++) { //finds average. - for (int j = 0; j < calcAverages[i].size(); j++) { - calcAverages[i][j].dist /= (float) iters; - } - } + if (m->debug) { m->mothurOut("[DEBUG]: found averages.\n"); } //create average tree for each calc for (int i = 0; i < calcDists.size(); i++) { @@ -896,7 +956,12 @@ int TreeGroupCommand::process(vector thisLookup) { } //create a new filename - string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave.tre"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile)); + variables["[calc]"] = treeCalculators[i]->getName(); + variables["[distance]"] = thisLookup[0]->getLabel(); + variables["[tag]"] = "ave"; + string outputFile = getOutputFileName("tree",variables); outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); //creates tree from similarity matrix and write out file @@ -904,12 +969,20 @@ int TreeGroupCommand::process(vector thisLookup) { if (newTree != NULL) { writeTree(outputFile, newTree); } } + if (m->debug) { m->mothurOut("[DEBUG]: done averages trees.\n"); } + //create all trees for each calc and find their consensus tree for (int i = 0; i < calcDists.size(); i++) { if (m->control_pressed) { break; } //create a new filename - string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all.tre"; + //create a new filename + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile)); + variables["[calc]"] = treeCalculators[i]->getName(); + variables["[distance]"] = thisLookup[0]->getLabel(); + variables["[tag]"] = "all"; + string outputFile = getOutputFileName("tree",variables); outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); ofstream outAll; @@ -929,7 +1002,7 @@ int TreeGroupCommand::process(vector thisLookup) { int row = calcDistsTotals[myIter][i][j].seq1; int column = calcDistsTotals[myIter][i][j].seq2; double dist = calcDistsTotals[myIter][i][j].dist; - + matrix[row][column] = dist; matrix[column][row] = dist; } @@ -944,13 +1017,18 @@ int TreeGroupCommand::process(vector thisLookup) { outAll.close(); if (m->control_pressed) { for (int k = 0; k < trees.size(); k++) { delete trees[k]; } } + if (m->debug) { m->mothurOut("[DEBUG]: done all trees.\n"); } + Consensus consensus; //clear old tree names if any m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups Tree* conTree = consensus.getTree(trees); + if (m->debug) { m->mothurOut("[DEBUG]: done cons tree.\n"); } + //create a new filename - string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons.tre"; + variables["[tag]"] = "cons"; + string conFile = getOutputFileName("tree",variables); outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile); ofstream outTree; m->openOutputFile(conFile, outTree); @@ -978,7 +1056,12 @@ int TreeGroupCommand::process(vector thisLookup) { } //create a new filename - string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile)); + variables["[calc]"] = treeCalculators[i]->getName(); + variables["[distance]"] = thisLookup[0]->getLabel(); + variables["[tag]"] = ""; + string outputFile = getOutputFileName("tree",variables); outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); //creates tree from similarity matrix and write out file