X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mgclustercommand.cpp;h=24c4f27777d21ed88b6f3b41411394502802404e;hp=b6c4164f0a49788145f47a3ea78f4f2244c168dc;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6 diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp index b6c4164..24c4f27 100644 --- a/mgclustercommand.cpp +++ b/mgclustercommand.cpp @@ -12,19 +12,20 @@ //********************************************************************************************************************** vector MGClusterCommand::setParameters(){ try { - CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); - CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength); - CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty); - CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff); - CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision); - CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "furthest", "", "", "",false,false); parameters.push_back(pmethod); - CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard); - CommandParameter pmin("min", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmin); - CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmerge); - CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phcluster); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(pblast); + 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 plength("length", "Number", "", "5", "", "", "","",false,false); parameters.push_back(plength); + CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "","",false,false); parameters.push_back(ppenalty); + CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "","",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", "average", "", "", "","",false,false); parameters.push_back(pmethod); + CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard); + CommandParameter pmin("min", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmin); + CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmerge); + CommandParameter phcluster("hcluster", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(phcluster); + 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); } @@ -44,7 +45,7 @@ string MGClusterCommand::getHelpString(){ helpString += "This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n"; helpString += "The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n"; helpString += "The precision parameter's default value is 100. \n"; - helpString += "The acceptable mgcluster methods are furthest, nearest and average. If no method is provided then furthest is assumed.\n\n"; + helpString += "The acceptable mgcluster methods are furthest, nearest and average. If no method is provided then average is assumed.\n"; helpString += "The min parameter allows you to specify is you want the minimum or maximum blast score ratio used in calculating the distance. The default is true, meaning you want the minimum.\n"; helpString += "The length parameter is used to specify the minimum overlap required. The default is 5.\n"; helpString += "The penalty parameter is used to adjust the error rate. The default is 0.10.\n"; @@ -52,7 +53,7 @@ string MGClusterCommand::getHelpString(){ helpString += "The hcluster parameter allows you to use the hcluster algorithm when clustering. This may be neccessary if your file is too large to fit into RAM. The default is false.\n"; helpString += "The mgcluster command should be in the following format: \n"; helpString += "mgcluster(blast=yourBlastfile, name=yourNameFile, cutoff=yourCutOff).\n"; - helpString += "Note: No spaces between parameter labels (i.e. balst), '=' and parameters (i.e.yourBlastfile).\n\n"; + helpString += "Note: No spaces between parameter labels (i.e. balst), '=' and parameters (i.e.yourBlastfile).\n"; return helpString; } catch(exception& e) { @@ -61,6 +62,23 @@ string MGClusterCommand::getHelpString(){ } } //********************************************************************************************************************** +string MGClusterCommand::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, "MGClusterCommand", "getOutputPattern"); + exit(1); + } +} +//******************************************************************************************************************* MGClusterCommand::MGClusterCommand(){ try { abort = true; calledHelp = true; @@ -82,6 +100,7 @@ MGClusterCommand::MGClusterCommand(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(); @@ -123,6 +142,14 @@ MGClusterCommand::MGClusterCommand(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; } + } } @@ -140,30 +167,38 @@ MGClusterCommand::MGClusterCommand(string option) { 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; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if (countfile != "" && namefile != "") { m->mothurOut("[ERROR]: Cannot have both a name file and count file. Please use one or the other."); m->mothurOutEndLine(); abort = true; } if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults string temp; - temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; } + temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; } precisionLength = temp.length(); - convert(temp, precision); + m->mothurConvert(temp, precision); temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "0.70"; } - 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")) { } else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; } temp = validParameter.validFile(parameters, "length", false); if (temp == "not found") { temp = "5"; } - convert(temp, length); + m->mothurConvert(temp, length); temp = validParameter.validFile(parameters, "penalty", false); if (temp == "not found") { temp = "0.10"; } - convert(temp, penalty); + m->mothurConvert(temp, penalty); temp = validParameter.validFile(parameters, "min", false); if (temp == "not found") { temp = "true"; } minWanted = m->isTrue(temp); @@ -174,8 +209,8 @@ MGClusterCommand::MGClusterCommand(string option) { temp = validParameter.validFile(parameters, "hcluster", false); if (temp == "not found") { temp = "false"; } hclusterWanted = m->isTrue(temp); - temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "F"; } - hard = m->isTrue(temp); + temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; } + hard = m->isTrue(temp); } } @@ -187,7 +222,6 @@ MGClusterCommand::MGClusterCommand(string option) { //********************************************************************************************************************** int MGClusterCommand::execute(){ try { - if (abort == true) { if (calledHelp) { return 0; } return 2; } //read names file @@ -200,15 +234,29 @@ int MGClusterCommand::execute(){ string tag = ""; time_t start; float previousDist = 0.00000; - float rndPreviousDist = 0.00000; - + float rndPreviousDist = 0.00000; + //read blastfile - creates sparsematrices for the distances and overlaps as well as a listvector //must remember to delete those objects here since readBlast does not read = new ReadBlast(blastfile, cutoff, penalty, length, minWanted, hclusterWanted); read->read(nameMap); - - list = new ListVector(nameMap->getListVector()); - RAbundVector* rabund = new RAbundVector(list->getRAbundVector()); + + list = new ListVector(nameMap->getListVector()); + RAbundVector* rabund = NULL; + + if(countfile != "") { + //map nameMapCounts = m->readNames(namefile); + ct = new CountTable(); + ct->readTable(countfile); + rabund = new RAbundVector(); + createRabund(ct, list, rabund); + }else { + rabund = new RAbundVector(list->getRAbundVector()); + } + + + //list = new ListVector(nameMap->getListVector()); + //rabund = new RAbundVector(list->getRAbundVector()); if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; } @@ -221,21 +269,32 @@ int MGClusterCommand::execute(){ else if (method == "nearest") { tag = "nn"; } else { tag = "an"; } - //open output files - m->openOutputFile(fileroot+ tag + ".list", listFile); - m->openOutputFile(fileroot+ tag + ".rabund", rabundFile); - m->openOutputFile(fileroot+ tag + ".sabund", sabundFile); + 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); + } + m->openOutputFile(listFileName, listFile); if (m->control_pressed) { delete nameMap; delete read; delete list; delete rabund; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } + double saveCutoff = cutoff; + if (!hclusterWanted) { //get distmatrix and overlap - SparseMatrix* distMatrix = read->getDistMatrix(); + SparseDistanceMatrix* distMatrix = read->getDistMatrix(); overlapMatrix = read->getOverlapMatrix(); //already sorted by read delete read; @@ -249,19 +308,22 @@ int MGClusterCommand::execute(){ if (m->control_pressed) { delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } - + + //cluster using cluster classes while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){ + if (m->debug) { cout << "numNodes=" << distMatrix->getNNodes() << " smallDist = " << distMatrix->getSmallDist() << endl; } + cluster->update(cutoff); if (m->control_pressed) { delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } @@ -284,7 +346,7 @@ int MGClusterCommand::execute(){ if (m->control_pressed) { delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } @@ -315,7 +377,7 @@ int MGClusterCommand::execute(){ if (m->control_pressed) { delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } @@ -345,7 +407,7 @@ int MGClusterCommand::execute(){ if (m->control_pressed) { delete nameMap; delete list; delete rabund; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } @@ -362,7 +424,7 @@ int MGClusterCommand::execute(){ if (m->control_pressed) { delete nameMap; delete list; delete rabund; delete hcluster; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } @@ -371,11 +433,16 @@ int MGClusterCommand::execute(){ seqs = hcluster->getSeqs(); + //to account for cutoff change in average neighbor + if (seqs.size() != 0) { + if (seqs[0].dist > cutoff) { break; } + } + if (m->control_pressed) { delete nameMap; delete list; delete rabund; delete hcluster; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); - remove(distFile.c_str()); - remove(overlapFile.c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); + m->mothurRemove(distFile); + m->mothurRemove(overlapFile); outputTypes.clear(); return 0; } @@ -384,13 +451,13 @@ int MGClusterCommand::execute(){ if (seqs[i].seq1 != seqs[i].seq2) { - hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist); + cutoff = hcluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist); if (m->control_pressed) { delete nameMap; delete list; delete rabund; delete hcluster; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); - remove(distFile.c_str()); - remove(overlapFile.c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); + m->mothurRemove(distFile); + m->mothurRemove(overlapFile); outputTypes.clear(); return 0; } @@ -412,9 +479,9 @@ int MGClusterCommand::execute(){ if (m->control_pressed) { delete nameMap; delete list; delete rabund; delete hcluster; delete temp; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); - remove(distFile.c_str()); - remove(overlapFile.c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); + m->mothurRemove(distFile); + m->mothurRemove(overlapFile); outputTypes.clear(); return 0; } @@ -448,9 +515,9 @@ int MGClusterCommand::execute(){ if (m->control_pressed) { delete nameMap; delete list; delete rabund; delete hcluster; delete temp; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); - remove(distFile.c_str()); - remove(overlapFile.c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); + m->mothurRemove(distFile); + m->mothurRemove(overlapFile); outputTypes.clear(); return 0; } @@ -465,30 +532,40 @@ int MGClusterCommand::execute(){ } delete hcluster; - remove(distFile.c_str()); - remove(overlapFile.c_str()); + m->mothurRemove(distFile); + m->mothurRemove(overlapFile); } - delete list; + delete list; delete rabund; listFile.close(); - sabundFile.close(); - rabundFile.close(); - + if (countfile == "") { + sabundFile.close(); + rabundFile.close(); + } if (m->control_pressed) { delete nameMap; - listFile.close(); rabundFile.close(); sabundFile.close(); remove((fileroot+ tag + ".list").c_str()); remove((fileroot+ tag + ".rabund").c_str()); remove((fileroot+ tag + ".sabund").c_str()); + listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - m->mothurOut(fileroot+ tag + ".list"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list"); - m->mothurOut(fileroot+ tag + ".rabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund"); - m->mothurOut(fileroot+ tag + ".sabund"); m->mothurOutEndLine(); outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund"); + m->mothurOut(listFileName); m->mothurOutEndLine(); outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName); + if (countfile == "") { + m->mothurOut(rabundFileName); m->mothurOutEndLine(); outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName); + m->mothurOut(sabundFileName); m->mothurOutEndLine(); outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName); + } m->mothurOutEndLine(); + 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"); @@ -522,12 +599,14 @@ int MGClusterCommand::execute(){ void MGClusterCommand::printData(ListVector* mergedList){ try { mergedList->print(listFile); - mergedList->getRAbundVector().print(rabundFile); - - SAbundVector sabund = mergedList->getSAbundVector(); + SAbundVector sabund = mergedList->getSAbundVector(); + + if (countfile == "") { + mergedList->getRAbundVector().print(rabundFile); + sabund.print(sabundFile); + } sabund.print(cout); - sabund.print(sabundFile); } catch(exception& e) { m->errorOut(e, "MGClusterCommand", "printData"); @@ -642,12 +721,12 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve try { //sort distFile string sortedDistFile = m->sortFile(unsortedDist, outputDir); - remove(unsortedDist.c_str()); //delete unsorted file + m->mothurRemove(unsortedDist); //delete unsorted file distFile = sortedDistFile; //sort overlap file string sortedOverlapFile = m->sortFile(unsortedOverlap, outputDir); - remove(unsortedOverlap.c_str()); //delete unsorted file + m->mothurRemove(unsortedOverlap); //delete unsorted file overlapFile = sortedOverlapFile; } catch(exception& e) { @@ -658,7 +737,33 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve //********************************************************************************************************************** +void MGClusterCommand::createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund){ + try { + //vector names = ct.getNamesOfSeqs(); + //for ( int i; i < ct.getNumGroups(); i++ ) { rav.push_back( ct.getNumSeqs(names[i]) ); } + //return rav; + + for(int i = 0; i < list->getNumBins(); i++) { + 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); + } + + + } + catch(exception& e) { + m->errorOut(e, "MGClusterCommand", "createRabund"); + exit(1); + } + +} +//**********************************************************************************************************************