X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clustercommand.cpp;h=94129654e1d2b11275e82d3a5da0382b1448efa9;hp=56ce8bb19e19d10b7181512b31d422d3d6b2a32f;hb=615301e57c25e241356a9c2380648d117709458d;hpb=0cefb55a2616975bd4a144fc345693695ffc9bb6 diff --git a/clustercommand.cpp b/clustercommand.cpp index 56ce8bb..9412965 100644 --- a/clustercommand.cpp +++ b/clustercommand.cpp @@ -13,21 +13,24 @@ #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); } @@ -42,8 +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; @@ -54,26 +58,21 @@ string ClusterCommand::getHelpString(){ } } //********************************************************************************************************************** -string ClusterCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string ClusterCommand::getOutputPattern(string type) { + try { + string pattern = ""; - //is this a type this command creates - it = outputTypes.find(type); - if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } - else { - if (type == "list") { outputFileName = "list"; } - else if (type == "rabund") { outputFileName = "rabund"; } - else if (type == "sabund") { outputFileName = "sabund"; } - else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } - } - return outputFileName; - } - catch(exception& e) { - m->errorOut(e, "ClusterCommand", "getOutputFileNameTag"); - exit(1); - } + 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(){ @@ -152,6 +151,14 @@ 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 @@ -169,6 +176,11 @@ ClusterCommand::ClusterCommand(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 == "")) { //is there are current file available for either of these? @@ -187,16 +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 @@ -213,10 +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"; } + //else { cutoffSet = true; } m->mothurConvert(temp, cutoff); - cutoff += (5 / (precision * 10.0)); + 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"; } @@ -253,6 +279,7 @@ int ClusterCommand::execute(){ //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"; } @@ -281,45 +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->getDMatrix(); - rabund = new RAbundVector(list->getRAbundVector()); + + 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++) { m->mothurRemove(outputNames[i]); } 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)); - string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund"); - string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund"); - string listFileName = fileroot+ tag + "." + getOutputFileNameTag("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); - m->openOutputFile(sabundFileName, sabundFile); - m->openOutputFile(rabundFileName, rabundFile); + 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(sabundFileName); outputTypes["sabund"].push_back(sabundFileName); - outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName); - outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName); + outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName); time_t estart = time(NULL); @@ -337,9 +378,8 @@ int ClusterCommand::execute(){ 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++) { m->mothurRemove(outputNames[i]); } 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)) { @@ -393,9 +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) { @@ -454,14 +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); } @@ -473,3 +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); + } + +} +//**********************************************************************************************************************