X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=hclustercommand.cpp;h=b991ccd6289b9afd44628c12bf451eb86529fa44;hp=128dee379080ddf32704367789c916d3bce14f41;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677 diff --git a/hclustercommand.cpp b/hclustercommand.cpp index 128dee3..b991ccd 100644 --- a/hclustercommand.cpp +++ b/hclustercommand.cpp @@ -10,51 +10,77 @@ #include "hclustercommand.h" //********************************************************************************************************************** -vector HClusterCommand::getValidParameters(){ +vector HClusterCommand::setParameters(){ try { - string Array[] = {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list-rabund-sabund",false,false,true); parameters.push_back(pphylip); + CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName","",false,false,true); parameters.push_back(pname); + CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list-rabund-sabund",false,false,true); parameters.push_back(pcolumn); + CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff); + CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision); + CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false); parameters.push_back(pmethod); + CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard); + CommandParameter psorted("sorted", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psorted); + CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund); + CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming); + 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); } return myArray; } catch(exception& e) { - m->errorOut(e, "HClusterCommand", "getValidParameters"); + m->errorOut(e, "HClusterCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -HClusterCommand::HClusterCommand(){ +string HClusterCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["list"] = tempOutNames; - outputTypes["rabund"] = tempOutNames; - outputTypes["sabund"] = tempOutNames; + string helpString = ""; + helpString += "The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required, unless you have valid current files.\n"; + helpString += "The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n"; + helpString += "The name parameter allows you to enter your name file and is required if your distance file is in column format. \n"; + helpString += "The hcluster command should be in the following format: \n"; + helpString += "hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n"; + helpString += "The acceptable hcluster methods are furthest, nearest, weighted and average.\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "HClusterCommand", "HClusterCommand"); + m->errorOut(e, "HClusterCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector HClusterCommand::getRequiredParameters(){ - try { - string Array[] = {"phylip","column","or"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "HClusterCommand", "getRequiredParameters"); - exit(1); - } +string HClusterCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "list") { pattern = "[filename],[clustertag],list"; } + else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; } + else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "HClusterCommand", "getOutputPattern"); + exit(1); + } } + //********************************************************************************************************************** -vector HClusterCommand::getRequiredFiles(){ +HClusterCommand::HClusterCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["list"] = tempOutNames; + outputTypes["rabund"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "HClusterCommand", "getRequiredFiles"); + m->errorOut(e, "HClusterCommand", "HClusterCommand"); exit(1); } } @@ -62,16 +88,14 @@ vector HClusterCommand::getRequiredFiles(){ //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen. HClusterCommand::HClusterCommand(string option) { try{ - globaldata = GlobalData::getInstance(); abort = false; calledHelp = false; //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -92,8 +116,6 @@ HClusterCommand::HClusterCommand(string option) { outputTypes["rabund"] = tempOutNames; outputTypes["sabund"] = tempOutNames; - globaldata->newRead(); - //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); if (inputDir == "not found"){ inputDir = ""; } @@ -131,22 +153,43 @@ HClusterCommand::HClusterCommand(string option) { phylipfile = validParameter.validFile(parameters, "phylip", true); if (phylipfile == "not open") { abort = true; } else if (phylipfile == "not found") { phylipfile = ""; } - else { distfile = phylipfile; format = "phylip"; } + else { distfile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); } columnfile = validParameter.validFile(parameters, "column", true); if (columnfile == "not open") { abort = true; } else if (columnfile == "not found") { columnfile = ""; } - else { distfile = columnfile; format = "column"; } + else { distfile = columnfile; format = "column"; m->setColumnFile(columnfile); } namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not open") { abort = true; } else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } - if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a hcluster command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; } + if ((phylipfile == "") && (columnfile == "")) { + //is there are current file available for either of these? + //give priority to column, then phylip + columnfile = m->getColumnFile(); + if (columnfile != "") { m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); } + else { + phylipfile = m->getPhylipFile(); + if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the hcluster command."); m->mothurOutEndLine(); + abort = true; + } + } + } else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; } if (columnfile != "") { - if (namefile == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; } + if (namefile == "") { + 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; + } + } } //check for optional parameter and set defaults @@ -157,18 +200,18 @@ HClusterCommand::HClusterCommand(string option) { if (temp == "not found") { temp = "100"; } //saves precision legnth for formatting below length = temp.length(); - convert(temp, precision); + m->mothurConvert(temp, precision); - temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; } + temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; } hard = m->isTrue(temp); temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } - convert(temp, cutoff); + m->mothurConvert(temp, cutoff); cutoff += (5 / (precision * 10.0)); method = validParameter.validFile(parameters, "method", false); - if (method == "not found") { method = "furthest"; } + if (method == "not found") { method = "average"; } if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { } else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average or weighted."); m->mothurOutEndLine(); abort = true; } @@ -193,14 +236,22 @@ HClusterCommand::HClusterCommand(string option) { else if (method == "nearest") { tag = "nn"; } else if (method == "weighted") { tag = "wn"; } else { tag = "an"; } + + map variables; + variables["[filename]"] = fileroot; + variables["[clustertag]"] = tag; - m->openOutputFile(fileroot+ tag + ".sabund", sabundFile); - m->openOutputFile(fileroot+ tag + ".rabund", rabundFile); - m->openOutputFile(fileroot+ tag + ".list", listFile); - - outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund"); - outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund"); - outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list"); + string sabundFileName = getOutputFileName("sabund",variables); + string rabundFileName = getOutputFileName("rabund",variables); + string listFileName = getOutputFileName("list", variables); + + m->openOutputFile(sabundFileName, sabundFile); + m->openOutputFile(rabundFileName, rabundFile); + m->openOutputFile(listFileName, listFile); + + outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName); + outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName); + outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName); } } } @@ -212,52 +263,30 @@ HClusterCommand::HClusterCommand(string option) { //********************************************************************************************************************** -void HClusterCommand::help(){ - try { - m->mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n"); - m->mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n"); - m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n"); - m->mothurOut("The hcluster command should be in the following format: \n"); - m->mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n"); - m->mothurOut("The acceptable hcluster methods are furthest, nearest, weighted and average.\n\n"); - } - catch(exception& e) { - m->errorOut(e, "HClusterCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -HClusterCommand::~HClusterCommand(){} - -//********************************************************************************************************************** - int HClusterCommand::execute(){ try { if (abort == true) { if (calledHelp) { return 0; } return 2; } + NameAssignment* nameMap = NULL; if(namefile != ""){ - globaldata->nameMap = new NameAssignment(namefile); - globaldata->nameMap->readMap(); - }else{ - globaldata->nameMap = NULL; - } + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + } time_t estart = time(NULL); if (!sorted) { read = new ReadCluster(distfile, cutoff, outputDir, true); read->setFormat(format); - read->read(globaldata->nameMap); + read->read(nameMap); if (m->control_pressed) { delete read; sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -266,14 +295,14 @@ int HClusterCommand::execute(){ list = read->getListVector(); delete read; }else { - list = new ListVector(globaldata->nameMap->getListVector()); + list = new ListVector(nameMap->getListVector()); } if (m->control_pressed) { sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -295,7 +324,7 @@ int HClusterCommand::execute(){ print_start = true; start = time(NULL); - cluster = new HCluster(rabund, list, method, distfile, globaldata->nameMap, cutoff); + cluster = new HCluster(rabund, list, method, distfile, nameMap, cutoff); vector seqs; seqs.resize(1); // to start loop if (m->control_pressed) { @@ -303,35 +332,41 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } + float saveCutoff = cutoff; while (seqs.size() != 0){ seqs = cluster->getSeqs(); + //to account for cutoff change in average neighbor + if (seqs.size() != 0) { + if (seqs[0].dist > cutoff) { break; } + } + if (m->control_pressed) { delete cluster; sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } for (int i = 0; i < seqs.size(); i++) { //-1 means skip me if (seqs[i].seq1 != seqs[i].seq2) { - cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist); + cutoff = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist); if (m->control_pressed) { delete cluster; sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -364,7 +399,7 @@ int HClusterCommand::execute(){ sabundFile.close(); rabundFile.close(); listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -374,28 +409,25 @@ int HClusterCommand::execute(){ else if(rndPreviousDistgListVector; globaldata->gListVector = NULL; - - //saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list - if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); } - else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); } - - globaldata->setListFile(fileroot+ tag + ".list"); - globaldata->setNameFile(""); - globaldata->setFormat("list"); - + sabundFile.close(); rabundFile.close(); listFile.close(); delete cluster; if (m->control_pressed) { - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } + + if (saveCutoff != cutoff) { + if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); } + else { saveCutoff = m->roundDist(saveCutoff, precision); } + + m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); + } + //set list file as new current listfile string current = ""; itTypes = outputTypes.find("list");