X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=1fa1a2833c1fa7604a9e2cbb07bf255ace9dcd94;hb=e88ba6b7a994a8502030d38cc5cc542994694d4d;hp=33a0e6dd9a3128541ab57777125251a97effdefc;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index 33a0e6d..1fa1a28 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -24,12 +24,12 @@ vector UnifracWeightedCommand::getValidParameters(){ //********************************************************************************************************************** UnifracWeightedCommand::UnifracWeightedCommand(){ try { - abort = true; - //initialize outputTypes + abort = true; calledHelp = true; vector tempOutNames; outputTypes["weighted"] = tempOutNames; outputTypes["wsummary"] = tempOutNames; outputTypes["phylip"] = tempOutNames; + outputTypes["column"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand"); @@ -64,11 +64,11 @@ vector UnifracWeightedCommand::getRequiredFiles(){ UnifracWeightedCommand::UnifracWeightedCommand(string option) { try { globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; Groups.clear(); //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command @@ -90,6 +90,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { outputTypes["weighted"] = tempOutNames; outputTypes["wsummary"] = tempOutNames; outputTypes["phylip"] = tempOutNames; + outputTypes["column"] = tempOutNames; if (globaldata->gTree.size() == 0) {//no trees were read m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true; } @@ -112,9 +113,13 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; } convert(itersString, iters); - string temp = validParameter.validFile(parameters, "distance", false); if (temp == "not found") { temp = "false"; } - phylip = m->isTrue(temp); - + string temp = validParameter.validFile(parameters, "distance", false); + if (temp == "not found") { phylip = false; outputForm = ""; } + else{ + if ((temp == "lt") || (temp == "column") || (temp == "square")) { phylip = true; outputForm = temp; } + else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; } + } + temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "F"; } random = m->isTrue(temp); @@ -175,13 +180,15 @@ void UnifracWeightedCommand::help(){ int UnifracWeightedCommand::execute() { try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } int start = time(NULL); //get weighted for users tree userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC... randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC... + + if (numComp < processors) { processors = numComp; } //get weighted scores for users trees for (int i = 0; i < T.size(); i++) { @@ -256,7 +263,7 @@ int UnifracWeightedCommand::execute() { if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } //report progress - m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine(); +// m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine(); } lines.clear(); @@ -326,7 +333,6 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > na try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) int process = 1; - int num = 0; vector processIDS; EstOutput results; @@ -349,7 +355,11 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector > na out.close(); exit(0); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); } + }else { + m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); + for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); } + exit(0); + } } driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, scores); @@ -493,15 +503,23 @@ void UnifracWeightedCommand::createPhylipFile() { //for each tree for (int i = 0; i < T.size(); i++) { - string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.dist"; - outputNames.push_back(phylipFileName); - outputTypes["phylip"].push_back(phylipFileName); + string phylipFileName; + if ((outputForm == "lt") || (outputForm == "square")) { + phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.phylip.dist"; + outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); + }else { //column + phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.column.dist"; + outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); + } + ofstream out; m->openOutputFile(phylipFileName, out); - //output numSeqs - out << globaldata->Groups.size() << endl; - + if ((outputForm == "lt") || (outputForm == "square")) { + //output numSeqs + out << globaldata->Groups.size() << endl; + } + //make matrix with scores in it vector< vector > dists; dists.resize(globaldata->Groups.size()); for (int i = 0; i < globaldata->Groups.size(); i++) { @@ -510,7 +528,7 @@ void UnifracWeightedCommand::createPhylipFile() { //flip it so you can print it for (int r=0; rGroups.size(); r++) { - for (int l = r+1; l < globaldata->Groups.size(); l++) { + for (int l = 0; l < r; l++) { dists[r][l] = utreeScores[count]; dists[l][r] = utreeScores[count]; count++; @@ -524,11 +542,30 @@ void UnifracWeightedCommand::createPhylipFile() { if (name.length() < 10) { //pad with spaces to make compatible while (name.length() < 10) { name += " "; } } - out << name << '\t'; - //output distances - for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; } - out << endl; + if (outputForm == "lt") { + out << name << '\t'; + + //output distances + for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; } + out << endl; + }else if (outputForm == "square") { + out << name << '\t'; + + //output distances + for (int l = 0; l < globaldata->Groups.size(); l++) { out << dists[r][l] << '\t'; } + out << endl; + }else{ + //output distances + for (int l = 0; l < r; l++) { + string otherName = globaldata->Groups[l]; + if (otherName.length() < 10) { //pad with spaces to make compatible + while (otherName.length() < 10) { otherName += " "; } + } + + out << name << '\t' << otherName << dists[r][l] << endl; + } + } } out.close(); }