X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustercommand.cpp;h=94129654e1d2b11275e82d3a5da0382b1448efa9;hp=25ab61b9f7068f7d5a36df3bd2e4596fd0905078;hb=615301e57c25e241356a9c2380648d117709458d;hpb=82bf18e3ef0a52345519f91a682e64cc385b56bb diff --git a/clustercommand.cpp b/clustercommand.cpp index 25ab61b..9412965 100644 --- a/clustercommand.cpp +++ b/clustercommand.cpp @@ -11,22 +11,26 @@ #include "readphylip.h" #include "readcolumn.h" #include "readmatrix.hpp" +#include "clusterdoturcommand.h" + //********************************************************************************************************************** vector ClusterCommand::setParameters(){ try { - 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 pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); 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 pshowabund("showabund", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshowabund); - CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptiming); - CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim); - CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","list",false,false,true); parameters.push_back(pphylip); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount); + CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","list",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,true); parameters.push_back(pmethod); + CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund); + CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming); + CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim); + CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + //CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust); + 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); } @@ -41,8 +45,9 @@ vector ClusterCommand::setParameters(){ string ClusterCommand::getHelpString(){ try { string helpString = ""; - helpString += "The cluster command parameter options are phylip, column, name, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n"; - helpString += "The cluster command should be in the following format: \n"; + helpString += "The cluster command parameter options are phylip, column, name, count, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n"; + //helpString += "The adjust parameter is used to handle missing distances. If you set a cutoff, adjust=f by default. If not, adjust=t by default. Adjust=f, means ignore missing distances and adjust cutoff as needed with the average neighbor method. Adjust=t, will treat missing distances as 1.0. You can also set the value the missing distances should be set to, adjust=0.5 would give missing distances a value of 0.5.\n"; + helpString += "The cluster command should be in the following format: \n"; helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n"; helpString += "The acceptable cluster methods are furthest, nearest, average and weighted. If no method is provided then average is assumed.\n"; return helpString; @@ -53,6 +58,23 @@ string ClusterCommand::getHelpString(){ } } //********************************************************************************************************************** +string ClusterCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],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, "ClusterCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** ClusterCommand::ClusterCommand(){ try { abort = true; calledHelp = true; @@ -75,6 +97,7 @@ ClusterCommand::ClusterCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -128,22 +151,36 @@ ClusterCommand::ClusterCommand(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 phylipfile = validParameter.validFile(parameters, "phylip", true); if (phylipfile == "not open") { phylipfile = ""; 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") { columnfile = ""; 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); } + + 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 == "")) { //is there are current file available for either of these? @@ -162,16 +199,22 @@ ClusterCommand::ClusterCommand(string option) { else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a cluster 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; + } } } } + if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... //get user cutoff and precision or use defaults @@ -180,7 +223,7 @@ ClusterCommand::ClusterCommand(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 = "T"; } hard = m->isTrue(temp); @@ -188,10 +231,18 @@ ClusterCommand::ClusterCommand(string option) { temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; } sim = m->isTrue(temp); + //bool cutoffSet = false; temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } - convert(temp, cutoff); - cutoff += (5 / (precision * 10.0)); + //else { cutoffSet = true; } + m->mothurConvert(temp, cutoff); + cutoff += (5 / (precision * 10.0)); + + //temp = validParameter.validFile(parameters, "adjust", false); if (temp == "not found") { temp = "F"; } + //if (m->isNumeric1(temp)) { m->mothurConvert(temp, adjust); } + //else if (m->isTrue(temp)) { adjust = 1.0; } + //else { adjust = -1.0; } + adjust=-1.0; method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "average"; } @@ -205,7 +256,7 @@ ClusterCommand::ClusterCommand(string option) { timing = validParameter.validFile(parameters, "timing", false); if (timing == "not found") { timing = "F"; } - } + } } catch(exception& e) { m->errorOut(e, "ClusterCommand", "ClusterCommand"); @@ -221,6 +272,35 @@ int ClusterCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } + //phylip file given and cutoff not given - use cluster.classic because it uses less memory and is faster + if ((format == "phylip") && (cutoff > 10.0)) { + m->mothurOutEndLine(); m->mothurOut("You are using a phylip file and no cutoff. I will run cluster.classic to save memory and time."); m->mothurOutEndLine(); + + //run unique.seqs for deconvolute results + string inputString = "phylip=" + distfile; + if (namefile != "") { inputString += ", name=" + namefile; } + else if (countfile != "") { inputString += ", count=" + countfile; } + inputString += ", precision=" + toString(precision); + inputString += ", method=" + method; + if (hard) { inputString += ", hard=T"; } + else { inputString += ", hard=F"; } + if (sim) { inputString += ", sim=T"; } + else { inputString += ", sim=F"; } + + + m->mothurOutEndLine(); + m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine(); + m->mothurOut("Running command: cluster.classic(" + inputString + ")"); m->mothurOutEndLine(); + + Command* clusterClassicCommand = new ClusterDoturCommand(inputString); + clusterClassicCommand->execute(); + delete clusterClassicCommand; + + m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine(); + + return 0; + } + ReadMatrix* read; if (format == "column") { read = new ReadColumnMatrix(columnfile, sim); } //sim indicates whether its a similarity matrix else if (format == "phylip") { read = new ReadPhylipMatrix(phylipfile, sim); } @@ -228,41 +308,59 @@ int ClusterCommand::execute(){ read->setCutoff(cutoff); NameAssignment* nameMap = NULL; + CountTable* ct = NULL; if(namefile != ""){ nameMap = new NameAssignment(namefile); nameMap->readMap(); - } + read->read(nameMap); + }else if (countfile != "") { + ct = new CountTable(); + ct->readTable(countfile, false); + read->read(ct); + }else { read->read(nameMap); } - read->read(nameMap); list = read->getListVector(); - matrix = read->getMatrix(); - rabund = new RAbundVector(list->getRAbundVector()); + matrix = read->getDMatrix(); + + if(countfile != "") { + rabund = new RAbundVector(); + createRabund(ct, list, rabund); //creates an rabund that includes the counts for the unique list + delete ct; + }else { rabund = new RAbundVector(list->getRAbundVector()); } delete read; if (m->control_pressed) { //clean up - delete list; delete matrix; delete rabund; - sabundFile.close();rabundFile.close();listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - return 0; + delete list; delete matrix; delete rabund; if(countfile == ""){rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } + listFile.close(); m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } //create cluster - if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); } - else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); } - else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix, cutoff, method); } - else if(method == "weighted"){ cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method); } + if (method == "furthest") { cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method, adjust); } + else if(method == "nearest"){ cluster = new SingleLinkage(rabund, list, matrix, cutoff, method, adjust); } + else if(method == "average"){ cluster = new AverageLinkage(rabund, list, matrix, cutoff, method, adjust); } + else if(method == "weighted"){ cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method, adjust); } tag = cluster->getTag(); if (outputDir == "") { outputDir += m->hasPath(distfile); } fileroot = outputDir + m->getRootName(m->getSimpleName(distfile)); - 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"); + map variables; + variables["[filename]"] = fileroot; + variables["[clustertag]"] = tag; + string sabundFileName = getOutputFileName("sabund", variables); + string rabundFileName = getOutputFileName("rabund", variables); + if (countfile != "") { variables["[tag2]"] = "unique_list"; } + string listFileName = getOutputFileName("list", variables); + + if (countfile == "") { + m->openOutputFile(sabundFileName, sabundFile); + m->openOutputFile(rabundFileName, rabundFile); + outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName); + outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName); + + } + m->openOutputFile(listFileName, listFile); + outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName); time_t estart = time(NULL); @@ -276,13 +374,12 @@ int ClusterCommand::execute(){ loops = 0; double saveCutoff = cutoff; - while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){ + while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){ if (m->control_pressed) { //clean up delete list; delete matrix; delete rabund; delete cluster; - sabundFile.close();rabundFile.close();listFile.close(); - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); - return 0; + if(countfile == "") {rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } + listFile.close(); m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } if (print_start && m->isTrue(timing)) { @@ -296,8 +393,8 @@ int ClusterCommand::execute(){ loops++; cluster->update(cutoff); - - float dist = matrix->getSmallDist(); + + float dist = matrix->getSmallDist(); float rndDist; if (hard) { rndDist = m->ceilDist(dist, precision); @@ -324,7 +421,7 @@ int ClusterCommand::execute(){ cout.flush(); print_start = false; } - + if(previousDist <= 0.0000){ printData("unique"); } @@ -336,9 +433,10 @@ int ClusterCommand::execute(){ delete list; delete rabund; delete cluster; - - sabundFile.close(); - rabundFile.close(); + if (countfile == "") { + sabundFile.close(); + rabundFile.close(); + } listFile.close(); if (saveCutoff != cutoff) { @@ -397,14 +495,17 @@ void ClusterCommand::printData(string label){ print_start = true; loops = 0; start = time(NULL); - - oldRAbund.setLabel(label); - if (m->isTrue(showabund)) { - oldRAbund.getSAbundVector().print(cout); - } - oldRAbund.print(rabundFile); - oldRAbund.getSAbundVector().print(sabundFile); - + + oldRAbund.setLabel(label); + if (countfile == "") { + oldRAbund.print(rabundFile); + oldRAbund.getSAbundVector().print(sabundFile); + } + + if (m->isTrue(showabund)) { + oldRAbund.getSAbundVector().print(cout); + } + oldList.setLabel(label); oldList.print(listFile); } @@ -416,3 +517,25 @@ void ClusterCommand::printData(string label){ } //********************************************************************************************************************** + +int ClusterCommand::createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund){ + try { + rabund->setLabel(list->getLabel()); + for(int i = 0; i < list->getNumBins(); i++) { + if (m->control_pressed) { break; } + vector binNames; + string bin = list->get(i); + m->splitAtComma(bin, binNames); + int total = 0; + for (int j = 0; j < binNames.size(); j++) { total += ct->getNumSeqs(binNames[j]); } + rabund->push_back(total); + } + return 0; + } + catch(exception& e) { + m->errorOut(e, "ClusterCommand", "createRabund"); + exit(1); + } + +} +//**********************************************************************************************************************