X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getoturepcommand.cpp;h=b8de5a62f6a8678c8b6f3e7f5de39b4da13aa817;hp=9742bcbd3b0ea952e3a5b5b54428bee701c5191f;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=4f2c7f477a1ef2d60a1c0c84ab1ba8243af67f87 diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp index 9742bcb..b8de5a6 100644 --- a/getoturepcommand.cpp +++ b/getoturepcommand.cpp @@ -39,21 +39,22 @@ inline bool compareGroup(repStruct left, repStruct right){ //********************************************************************************************************************** vector GetOTURepCommand::setParameters(){ try { - CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup); - CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname); - CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff); - CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision); - CommandParameter pweighted("weighted", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pweighted); - CommandParameter psorted("sorted", "Multiple", "none-name-bin-size-group", "none", "", "", "",false,false); parameters.push_back(psorted); - CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","name",false,true, true); parameters.push_back(plist); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,false, true); parameters.push_back(pfasta); + CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false, true); parameters.push_back(pphylip); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false, true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "ColumnName","count",false,false, true); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false, true); parameters.push_back(pgroup); + CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","",false,false, true); parameters.push_back(pcolumn); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff); + CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision); + CommandParameter pweighted("weighted", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pweighted); + CommandParameter psorted("sorted", "Multiple", "none-name-bin-size-group", "none", "", "", "","",false,false); parameters.push_back(psorted); + CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge); + 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); } @@ -68,9 +69,9 @@ vector GetOTURepCommand::setParameters(){ string GetOTURepCommand::getHelpString(){ try { string helpString = ""; - helpString += "The get.oturep command parameters are phylip, column, list, fasta, name, group, large, weighted, cutoff, precision, groups, sorted and label. The fasta and list parameters are required, as well as phylip or column and name, unless you have valid current files.\n"; + helpString += "The get.oturep command parameters are phylip, column, list, fasta, name, group, count, large, weighted, cutoff, precision, groups, sorted and label. The list parameter is required, as well as phylip or column and name, unless you have valid current files.\n"; helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n"; - helpString += "The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. \n"; + helpString += "The phylip or column parameter is required, but only one may be used. If you use a column file the name or count filename is required. \n"; helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n"; helpString += "The get.oturep command should be in the following format: get.oturep(phylip=yourDistanceMatrix, fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n"; helpString += "Example get.oturep(phylip=amazon.dist, fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups).\n"; @@ -95,6 +96,23 @@ string GetOTURepCommand::getHelpString(){ } } //********************************************************************************************************************** +string GetOTURepCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],[tag],rep.fasta-[filename],[tag],[group],rep.fasta"; } + else if (type == "name") { pattern = "[filename],[tag],rep.names-[filename],[tag],[group],rep.names"; } + else if (type == "count") { pattern = "[filename],[tag],rep.count_table-[filename],[tag],[group],rep.count_table"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "GetOTURepCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** GetOTURepCommand::GetOTURepCommand(){ try { abort = true; calledHelp = true; @@ -102,6 +120,7 @@ GetOTURepCommand::GetOTURepCommand(){ vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["name"] = tempOutNames; + outputTypes["count"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "GetOTURepCommand", "GetOTURepCommand"); @@ -136,6 +155,7 @@ GetOTURepCommand::GetOTURepCommand(string option) { vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["name"] = tempOutNames; + outputTypes["count"] = tempOutNames; //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); @@ -189,6 +209,14 @@ GetOTURepCommand::GetOTURepCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["group"] = 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; } + } } @@ -197,11 +225,7 @@ GetOTURepCommand::GetOTURepCommand(string option) { //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not found") { - fastafile = m->getFastaFile(); - if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); } - else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } - } + if (fastafile == "not found") { fastafile = ""; } else if (fastafile == "not open") { abort = true; } else { m->setFastaFile(fastafile); } @@ -228,6 +252,24 @@ GetOTURepCommand::GetOTURepCommand(string option) { if (namefile == "not open") { abort = true; } else if (namefile == "not found") { namefile = ""; } else { m->setNameFile(namefile); } + + hasGroups = false; + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not found") { countfile = ""; } + else if (countfile == "not open") { abort = true; countfile = ""; } + else { + m->setCountTableFile(countfile); + ct.readTable(countfile); + if (ct.hasGroupInfo()) { hasGroups = true; } + } + + if ((namefile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true; + } + + if ((groupfile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true; + } if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these? //give priority to column, then phylip @@ -244,14 +286,18 @@ GetOTURepCommand::GetOTURepCommand(string option) { }else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a get.oturep command you must enter ONLY ONE of the following: phylip or column."); 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 @@ -275,15 +321,15 @@ GetOTURepCommand::GetOTURepCommand(string option) { sorted = ""; } - if ((sorted == "group") && (groupfile == "")) { - m->mothurOut("You must provide a groupfile to sort by group. I will not sort."); m->mothurOutEndLine(); + if ((sorted == "group") && ((groupfile == "")&& !hasGroups)) { + m->mothurOut("You must provide a groupfile or have a count file with group info to sort by group. I will not sort."); m->mothurOutEndLine(); sorted = ""; } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - if (groupfile == "") { + if ((groupfile == "") && (!hasGroups)) { m->mothurOut("You must provide a groupfile to use groups."); m->mothurOutEndLine(); abort = true; }else { @@ -301,10 +347,10 @@ GetOTURepCommand::GetOTURepCommand(string option) { if ((weighted) && (namefile == "")) { m->mothurOut("You cannot set weighted to true unless you provide a namesfile."); m->mothurOutEndLine(); abort = true; } temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; } - convert(temp, precision); + m->mothurConvert(temp, precision); temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10.0"; } - convert(temp, cutoff); + m->mothurConvert(temp, cutoff); cutoff += (5 / (precision * 10.0)); } } @@ -323,103 +369,9 @@ int GetOTURepCommand::execute(){ int error; list = NULL; - if (!large) { - //read distance files - if (format == "column") { readMatrix = new ReadColumnMatrix(distFile); } - else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(distFile); } - else { m->mothurOut("File format error."); m->mothurOutEndLine(); return 0; } - - readMatrix->setCutoff(cutoff); - - if(namefile != ""){ - nameMap = new NameAssignment(namefile); - nameMap->readMap(); - }else{ nameMap = NULL; } - - readMatrix->read(nameMap); - - if (m->control_pressed) { delete readMatrix; return 0; } - - list = readMatrix->getListVector(); - - SparseMatrix* matrix = readMatrix->getMatrix(); - - // Create a data structure to quickly access the distance information. - // It consists of a vector of distance maps, where each map contains - // all distances of a certain sequence. Vector and maps are accessed - // via the index of a sequence in the distance matrix - seqVec = vector(list->size()); - for (MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++) { - if (m->control_pressed) { delete readMatrix; return 0; } - seqVec[currentCell->row][currentCell->column] = currentCell->dist; - } - //add dummy map for unweighted calc - SeqMap dummy; - seqVec.push_back(dummy); - - delete matrix; - delete readMatrix; - delete nameMap; - - if (m->control_pressed) { return 0; } - }else { - //process file and set up indexes - if (format == "column") { formatMatrix = new FormatColumnMatrix(distFile); } - else if (format == "phylip") { formatMatrix = new FormatPhylipMatrix(distFile); } - else { m->mothurOut("File format error."); m->mothurOutEndLine(); return 0; } - - formatMatrix->setCutoff(cutoff); - - if(namefile != ""){ - nameMap = new NameAssignment(namefile); - nameMap->readMap(); - }else{ nameMap = NULL; } - - formatMatrix->read(nameMap); - - if (m->control_pressed) { delete formatMatrix; return 0; } - - list = formatMatrix->getListVector(); - - distFile = formatMatrix->getFormattedFileName(); - - //positions in file where the distances for each sequence begin - //rowPositions[1] = position in file where distance related to sequence 1 start. - rowPositions = formatMatrix->getRowPositions(); - rowPositions.push_back(-1); //dummy row for unweighted calc - - delete formatMatrix; - delete nameMap; - - //openfile for getMap to use - m->openInputFile(distFile, inRow); - - if (m->control_pressed) { inRow.close(); m->mothurRemove(distFile); return 0; } - } - - - //list bin 0 = first name read in distance matrix, list bin 1 = second name read in distance matrix - if (list != NULL) { - vector names; - string binnames; - //map names to rows in sparsematrix - for (int i = 0; i < list->size(); i++) { - names.clear(); - binnames = list->get(i); - - m->splitAtComma(binnames, names); - - for (int j = 0; j < names.size(); j++) { - nameToIndex[names[j]] = i; - } - } - } else { m->mothurOut("error, no listvector."); m->mothurOutEndLine(); } - + readDist(); - if (m->control_pressed) { - if (large) { inRow.close(); m->mothurRemove(distFile); } - return 0; - } + if (m->control_pressed) { if (large) { inRow.close(); m->mothurRemove(distFile); } return 0; } if (groupfile != "") { //read in group map info. @@ -428,13 +380,18 @@ int GetOTURepCommand::execute(){ if (error == 1) { delete groupMap; m->mothurOut("Error reading your groupfile. Proceeding without groupfile."); m->mothurOutEndLine(); groupfile = ""; } if (Groups.size() != 0) { - SharedUtil* util = new SharedUtil(); + SharedUtil util; vector gNamesOfGroups = groupMap->getNamesOfGroups(); - util->setGroups(Groups, gNamesOfGroups, "getoturep"); + util.setGroups(Groups, gNamesOfGroups, "getoturep"); groupMap->setNamesOfGroups(gNamesOfGroups); - delete util; } - } + }else if (hasGroups) { + if (Groups.size() != 0) { + SharedUtil util; + vector gNamesOfGroups = ct.getNamesOfGroups(); + util.setGroups(Groups, gNamesOfGroups, "getoturep"); + } + } //done with listvector from matrix if (list != NULL) { delete list; } @@ -537,21 +494,30 @@ int GetOTURepCommand::execute(){ if (!weighted) { nameFileMap.clear(); } - //read fastafile - fasta = new FastaMap(); - fasta->readFastaFile(fastafile); - - //if user gave a namesfile then use it - if (namefile != "") { readNamesFile(); } - - //output create and output the .rep.fasta files - map::iterator itNameFile; - for (itNameFile = outputNameFiles.begin(); itNameFile != outputNameFiles.end(); itNameFile++) { - processNames(itNameFile->first, itNameFile->second); + + if (fastafile != "") { + //read fastafile + fasta = new FastaMap(); + fasta->readFastaFile(fastafile); + + //if user gave a namesfile then use it + if (namefile != "") { readNamesFile(); } + + //output create and output the .rep.fasta files + map::iterator itNameFile; + for (itNameFile = outputNameFiles.begin(); itNameFile != outputNameFiles.end(); itNameFile++) { + processFastaNames(itNameFile->first, itNameFile->second); + } + }else { + //output create and output the .rep.fasta files + map::iterator itNameFile; + for (itNameFile = outputNameFiles.begin(); itNameFile != outputNameFiles.end(); itNameFile++) { + processNames(itNameFile->first, itNameFile->second); + } } - delete fasta; - if (groupfile != "") { delete groupMap; } + + if (groupfile != "") { delete groupMap; } if (m->control_pressed) { return 0; } @@ -566,6 +532,11 @@ int GetOTURepCommand::execute(){ if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } } + + itTypes = outputTypes.find("count"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); } + } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -579,7 +550,120 @@ int GetOTURepCommand::execute(){ exit(1); } } +//********************************************************************************************************************** +int GetOTURepCommand::readDist() { + try { + + if (!large) { + //read distance files + if (format == "column") { readMatrix = new ReadColumnMatrix(distFile); } + else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(distFile); } + else { m->mothurOut("File format error."); m->mothurOutEndLine(); return 0; } + + readMatrix->setCutoff(cutoff); + + NameAssignment* nameMap = NULL; + if(namefile != ""){ + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + readMatrix->read(nameMap); + }else if (countfile != "") { + readMatrix->read(&ct); + }else { + readMatrix->read(nameMap); + } + + if (m->control_pressed) { delete readMatrix; return 0; } + + list = readMatrix->getListVector(); + SparseDistanceMatrix* matrix = readMatrix->getDMatrix(); + + // Create a data structure to quickly access the distance information. + // It consists of a vector of distance maps, where each map contains + // all distances of a certain sequence. Vector and maps are accessed + // via the index of a sequence in the distance matrix + seqVec = vector(list->size()); + for (int i = 0; i < matrix->seqVec.size(); i++) { + for (int j = 0; j < matrix->seqVec[i].size(); j++) { + if (m->control_pressed) { delete readMatrix; return 0; } + //already added everyone else in row + if (i < matrix->seqVec[i][j].index) { seqVec[i][matrix->seqVec[i][j].index] = matrix->seqVec[i][j].dist; } + } + } + //add dummy map for unweighted calc + SeqMap dummy; + seqVec.push_back(dummy); + + delete matrix; + delete readMatrix; + delete nameMap; + + if (m->control_pressed) { return 0; } + }else { + //process file and set up indexes + if (format == "column") { formatMatrix = new FormatColumnMatrix(distFile); } + else if (format == "phylip") { formatMatrix = new FormatPhylipMatrix(distFile); } + else { m->mothurOut("File format error."); m->mothurOutEndLine(); return 0; } + + formatMatrix->setCutoff(cutoff); + + NameAssignment* nameMap = NULL; + if(namefile != ""){ + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + formatMatrix->read(nameMap); + }else if (countfile != "") { + formatMatrix->read(&ct); + }else { + formatMatrix->read(nameMap); + } + + if (m->control_pressed) { delete formatMatrix; return 0; } + + list = formatMatrix->getListVector(); + distFile = formatMatrix->getFormattedFileName(); + + //positions in file where the distances for each sequence begin + //rowPositions[1] = position in file where distance related to sequence 1 start. + rowPositions = formatMatrix->getRowPositions(); + rowPositions.push_back(-1); //dummy row for unweighted calc + + delete formatMatrix; + delete nameMap; + + //openfile for getMap to use + m->openInputFile(distFile, inRow); + + if (m->control_pressed) { inRow.close(); m->mothurRemove(distFile); return 0; } + } + + + //list bin 0 = first name read in distance matrix, list bin 1 = second name read in distance matrix + if (list != NULL) { + vector names; + string binnames; + //map names to rows in sparsematrix + for (int i = 0; i < list->size(); i++) { + names.clear(); + binnames = list->get(i); + + m->splitAtComma(binnames, names); + + for (int j = 0; j < names.size(); j++) { + nameToIndex[names[j]] = i; + } + } + } else { m->mothurOut("error, no listvector."); m->mothurOutEndLine(); } + if (m->control_pressed) { if (large) { inRow.close(); m->mothurRemove(distFile); }return 0; } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "GetOTURepCommand", "execute"); + exit(1); + } +} //********************************************************************************************************************** void GetOTURepCommand::readNamesFile() { try { @@ -648,32 +732,38 @@ void GetOTURepCommand::readNamesFile(bool w) { } } //********************************************************************************************************************** -string GetOTURepCommand::findRep(vector names) { +string GetOTURepCommand::findRep(vector names, string group) { try{ // if only 1 sequence in bin or processing the "unique" label, then // the first sequence of the OTU is the representative one if ((names.size() == 1)) { return names[0]; }else{ - vector seqIndex(names.size()); - vector max_dist(names.size()); - vector total_dist(names.size()); + vector seqIndex; //(names.size()); map::iterator itNameFile; map::iterator itNameIndex; //fill seqIndex and initialize sums for (size_t i = 0; i < names.size(); i++) { if (weighted) { - seqIndex[i] = nameToIndex[names[i]]; + seqIndex.push_back(nameToIndex[names[i]]); + if (countfile != "") { //if countfile is not blank then we can assume the list file contains only uniques, otherwise we assume list file contains everyone. + int numRep = 0; + if (group != "") { numRep = ct.getGroupCount(names[i], group); } + else { numRep = ct.getGroupCount(names[i]); } + for (int j = 1; j < numRep; j++) { //don't add yourself again + seqIndex.push_back(nameToIndex[names[i]]); + } + } }else { if (namefile == "") { itNameIndex = nameToIndex.find(names[i]); if (itNameIndex == nameToIndex.end()) { // you are not in the distance file and no namesfile, then assume you are not unique - if (large) { seqIndex[i] = (rowPositions.size()-1); } - else { seqIndex[i] = (seqVec.size()-1); } + if (large) { seqIndex.push_back((rowPositions.size()-1)); } + else { seqIndex.push_back((seqVec.size()-1)); } }else { - seqIndex[i] = itNameIndex->second; + seqIndex.push_back(itNameIndex->second); } }else { @@ -686,17 +776,18 @@ string GetOTURepCommand::findRep(vector names) { string name2 = itNameFile->second; if (name1 == name2) { //then you are unique so add your real dists - seqIndex[i] = nameToIndex[names[i]]; + seqIndex.push_back(nameToIndex[names[i]]); }else { //add dummy - if (large) { seqIndex[i] = (rowPositions.size()-1); } - else { seqIndex[i] = (seqVec.size()-1); } + if (large) { seqIndex.push_back((rowPositions.size()-1)); } + else { seqIndex.push_back((seqVec.size()-1)); } } } } } - max_dist[i] = 0.0; - total_dist[i] = 0.0; } + + vector max_dist(seqIndex.size(), 0.0); + vector total_dist(seqIndex.size(), 0.0); // loop through all entries in seqIndex SeqMap::iterator it; @@ -765,20 +856,39 @@ int GetOTURepCommand::process(ListVector* processList) { string outputNamesFile; map filehandles; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); + if (Groups.size() == 0) { //you don't want to use groups - outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".rep.names"; - m->openOutputFile(outputNamesFile, newNamesOutput); - outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); + variables["[tag]"] = processList->getLabel(); + if (countfile == "") { + outputNamesFile = getOutputFileName("name", variables); + outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); + }else { + outputNamesFile = getOutputFileName("count", variables); + outputNames.push_back(outputNamesFile); outputTypes["count"].push_back(outputNamesFile); + } outputNameFiles[outputNamesFile] = processList->getLabel(); + m->openOutputFile(outputNamesFile, newNamesOutput); + newNamesOutput << "noGroup" << endl; }else{ //you want to use groups ofstream* temp; for (int i=0; igetLabel(); + variables["[group]"] = Groups[i]; filehandles[Groups[i]] = temp; - outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names"; + outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + "."; + if (countfile == "") { + outputNamesFile = getOutputFileName("name", variables); + outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); + }else { + outputNamesFile = getOutputFileName("count", variables); + outputNames.push_back(outputNamesFile); outputTypes["count"].push_back(outputNamesFile); + } m->openOutputFile(outputNamesFile, *(temp)); - outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); + *(temp) << Groups[i] << endl; outputNameFiles[outputNamesFile] = processList->getLabel() + "." + Groups[i]; } } @@ -803,7 +913,7 @@ int GetOTURepCommand::process(ListVector* processList) { m->splitAtComma(temp, namesInBin); if (Groups.size() == 0) { - nameRep = findRep(namesInBin); + nameRep = findRep(namesInBin, ""); newNamesOutput << i << '\t' << nameRep << '\t' << processList->get(i) << endl; }else{ map > NamesInGroup; @@ -812,20 +922,25 @@ int GetOTURepCommand::process(ListVector* processList) { } for (int j=0; jgetGroup(namesInBin[j]); - - if (thisgroup == "not found") { m->mothurOut(namesInBin[j] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } - - if (m->inUsersGroups(thisgroup, Groups)) { //add this name to correct group - NamesInGroup[thisgroup].push_back(namesInBin[j]); - } + if (groupfile != "") { + string thisgroup = groupMap->getGroup(namesInBin[j]); + if (thisgroup == "not found") { m->mothurOut(namesInBin[j] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; } + + //add this name to correct group + if (m->inUsersGroups(thisgroup, Groups)) { NamesInGroup[thisgroup].push_back(namesInBin[j]); } + }else { + vector thisSeqsGroups = ct.getGroups(namesInBin[j]); + for (int k = 0; k < thisSeqsGroups.size(); k++) { + if (m->inUsersGroups(thisSeqsGroups[k], Groups)) { NamesInGroup[thisSeqsGroups[k]].push_back(namesInBin[j]); } + } + } } //get rep for each group in otu for (int j=0; jhasPath(listfile); } - string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + ".rep.fasta"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[tag]"] = label; + string outputFileName = getOutputFileName("fasta",variables); m->openOutputFile(outputFileName, out); vector reps; outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); @@ -871,28 +989,51 @@ int GetOTURepCommand::processNames(string filename, string label) { ofstream out2; string tempNameFile = filename + ".temp"; m->openOutputFile(tempNameFile, out2); - + ifstream in; m->openInputFile(filename, in); int i = 0; + string tempGroup = ""; + in >> tempGroup; m->gobble(in); + + CountTable thisCt; + if (countfile != "") { + thisCt.readTable(countfile); + if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; } + } + + int thistotal = 0; while (!in.eof()) { string rep, binnames; in >> i >> rep >> binnames; m->gobble(in); - out2 << rep << '\t' << binnames << endl; vector names; m->splitAtComma(binnames, names); int binsize = names.size(); - + + if (countfile == "") { out2 << rep << '\t' << binnames << endl; } + else { + if (tempGroup == "noGroup") { + for (int j = 0; j < names.size(); j++) { + if (names[j] != rep) { thisCt.mergeCounts(rep, names[j]); } + } + binsize = thisCt.getNumSeqs(rep); + }else { + int total = 0; + for (int j = 0; j < names.size(); j++) { total += thisCt.getGroupCount(names[j], tempGroup); } + out2 << rep << '\t' << total << '\t' << total << endl; + binsize = total; + } + } + thistotal += binsize; //if you have a groupfile string group = ""; + map groups; + map::iterator groupIt; if (groupfile != "") { - map groups; - map::iterator groupIt; - //find the groups that are in this bin - for (size_t i = 0; i < names.size(); i++) { + for (int i = 0; i < names.size(); i++) { string groupName = groupMap->getGroup(names[i]); if (groupName == "not found") { m->mothurOut(names[i] + " is missing from your group file. Please correct. "); m->mothurOutEndLine(); @@ -908,7 +1049,21 @@ int GetOTURepCommand::processNames(string filename, string label) { } //rip off last dash group = group.substr(0, group.length()-1); - }else{ group = ""; } + }else if (hasGroups) { + map groups; + for (int i = 0; i < names.size(); i++) { + vector thisSeqsGroups = ct.getGroups(names[i]); + for (int j = 0; j < thisSeqsGroups.size(); j++) { groups[thisSeqsGroups[j]] = thisSeqsGroups[j]; } + } + //turn the groups into a string + for (groupIt = groups.begin(); groupIt != groups.end(); groupIt++) { + group += groupIt->first + "-"; + } + //rip off last dash + group = group.substr(0, group.length()-1); + //cout << group << endl; + } + else{ group = ""; } //print out name and sequence for that bin @@ -918,7 +1073,7 @@ int GetOTURepCommand::processNames(string filename, string label) { if (sorted == "") { //print them out rep = rep + "\t" + toString(i+1); rep = rep + "|" + toString(binsize); - if (groupfile != "") { + if (group != "") { rep = rep + "|" + group; } out << ">" << rep << endl; @@ -944,7 +1099,7 @@ int GetOTURepCommand::processNames(string filename, string label) { string sequence = fasta->getSequence(reps[i].name); string outputName = reps[i].name + "\t" + toString(reps[i].bin); outputName = outputName + "|" + toString(reps[i].size); - if (groupfile != "") { + if (reps[i].group != "") { outputName = outputName + "|" + reps[i].group; } out << ">" << outputName << endl; @@ -955,13 +1110,76 @@ int GetOTURepCommand::processNames(string filename, string label) { in.close(); out.close(); out2.close(); - + m->mothurRemove(filename); rename(tempNameFile.c_str(), filename.c_str()); + + if ((countfile != "") && (tempGroup == "noGroup")) { thisCt.printTable(filename); } return 0; } + catch(exception& e) { + m->errorOut(e, "GetOTURepCommand", "processFastaNames"); + exit(1); + } +} +//********************************************************************************************************************** +int GetOTURepCommand::processNames(string filename, string label) { + try{ + + //create output file + if (outputDir == "") { outputDir += m->hasPath(listfile); } + + ofstream out2; + string tempNameFile = filename + ".temp"; + m->openOutputFile(tempNameFile, out2); + + ifstream in; + m->openInputFile(filename, in); + + int i = 0; + string rep, binnames; + + string tempGroup = ""; + in >> tempGroup; m->gobble(in); + + CountTable thisCt; + if (countfile != "") { + thisCt.readTable(countfile); + if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; } + } + + while (!in.eof()) { + if (m->control_pressed) { break; } + in >> i >> rep >> binnames; m->gobble(in); + + if (countfile == "") { out2 << rep << '\t' << binnames << endl; } + else { + vector names; + m->splitAtComma(binnames, names); + if (tempGroup == "noGroup") { + for (int j = 0; j < names.size(); j++) { + if (names[j] != rep) { thisCt.mergeCounts(rep, names[j]); } + } + }else { + int total = 0; + for (int j = 0; j < names.size(); j++) { total += thisCt.getGroupCount(names[j], tempGroup); } + out2 << rep << '\t' << total << '\t' << total << endl; + } + } + + } + in.close(); + out2.close(); + + m->mothurRemove(filename); + rename(tempNameFile.c_str(), filename.c_str()); + + if ((countfile != "") && (tempGroup == "noGroup")) { thisCt.printTable(filename); } + + return 0; + } catch(exception& e) { m->errorOut(e, "GetOTURepCommand", "processNames"); exit(1);