X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=8019def31cad9acc54c1308171bf796e949890a1;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=16348c8d324a962ca336c82a2ad303f156cde9e3;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git diff --git a/clustercommand.cpp b/clustercommand.cpp index 16348c8..8019def 100644 --- a/clustercommand.cpp +++ b/clustercommand.cpp @@ -11,6 +11,7 @@ #include "readphylip.h" #include "readcolumn.h" #include "readmatrix.hpp" +#include "clusterdoturcommand.h" //********************************************************************************************************************** vector ClusterCommand::setParameters(){ @@ -53,6 +54,28 @@ string ClusterCommand::getHelpString(){ } } //********************************************************************************************************************** +string ClusterCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //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); + } +} +//********************************************************************************************************************** ClusterCommand::ClusterCommand(){ try { abort = true; calledHelp = true; @@ -135,16 +158,17 @@ ClusterCommand::ClusterCommand(string option) { 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); } if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these? @@ -181,7 +205,7 @@ 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); @@ -191,7 +215,7 @@ ClusterCommand::ClusterCommand(string option) { 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); @@ -206,7 +230,7 @@ ClusterCommand::ClusterCommand(string option) { timing = validParameter.validFile(parameters, "timing", false); if (timing == "not found") { timing = "F"; } - } + } } catch(exception& e) { m->errorOut(e, "ClusterCommand", "ClusterCommand"); @@ -222,6 +246,34 @@ 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; } + 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); } @@ -243,7 +295,7 @@ int ClusterCommand::execute(){ 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(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -257,13 +309,17 @@ int ClusterCommand::execute(){ 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); + string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund"); + string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund"); + string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list"); + + m->openOutputFile(sabundFileName, sabundFile); + m->openOutputFile(rabundFileName, rabundFile); + m->openOutputFile(listFileName, 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"); + 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); time_t estart = time(NULL); @@ -282,7 +338,7 @@ 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++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } @@ -325,7 +381,7 @@ int ClusterCommand::execute(){ cout.flush(); print_start = false; } - + if(previousDist <= 0.0000){ printData("unique"); }