//**********************************************************************************************************************
-TreeGroupCommand::TreeGroupCommand(){
+TreeGroupCommand::TreeGroupCommand(string option){
try {
globaldata = GlobalData::getInstance();
- format = globaldata->getFormat();
- validCalculator = new ValidCalculators();
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+ Groups.clear();
+ Estimators.clear();
- if (format == "sharedfile") {
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "jabund") {
- treeCalculators.push_back(new JAbund());
- }else if (globaldata->Estimators[i] == "sorabund") {
- treeCalculators.push_back(new SorAbund());
- }else if (globaldata->Estimators[i] == "jclass") {
- treeCalculators.push_back(new Jclass());
- }else if (globaldata->Estimators[i] == "sorclass") {
- treeCalculators.push_back(new SorClass());
- }else if (globaldata->Estimators[i] == "jest") {
- treeCalculators.push_back(new Jest());
- }else if (globaldata->Estimators[i] == "sorest") {
- treeCalculators.push_back(new SorEst());
- }else if (globaldata->Estimators[i] == "thetayc") {
- treeCalculators.push_back(new ThetaYC());
- }else if (globaldata->Estimators[i] == "thetan") {
- treeCalculators.push_back(new ThetaN());
- }else if (globaldata->Estimators[i] == "morisitahorn") {
- treeCalculators.push_back(new MorHorn());
- }else if (globaldata->Estimators[i] == "braycurtis") {
- treeCalculators.push_back(new BrayCurtis());
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"line","label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser. getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { format = "phylip"; }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { format = "column"; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { globaldata->setNameFile(namefile); }
+
+ format = globaldata->getFormat();
+
+ //error checking on files
+ if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
+
+ if (columnfile != "") {
+ if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ line = validParameter.validFile(parameters, "line", false);
+ if (line == "not found") { line = ""; }
+ else {
+ if(line != "all") { splitAtDash(line, lines); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //make sure user did not use both the line and label parameters
+ if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
+ //if the user has not specified any line or labels use the ones from read.otu
+ else if((line == "") && (label == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jclass-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jclass-thetayc"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
+ convert(temp, precision);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, cutoff);
+ cutoff += (5 / (precision * 10.0));
+
+
+ if (abort == false) {
+
+ validCalculator = new ValidCalculators();
+
+ if (format == "sharedfile") {
+ int i;
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
+ if (Estimators[i] == "jabund") {
+ treeCalculators.push_back(new JAbund());
+ }else if (Estimators[i] == "sorabund") {
+ treeCalculators.push_back(new SorAbund());
+ }else if (Estimators[i] == "jclass") {
+ treeCalculators.push_back(new Jclass());
+ }else if (Estimators[i] == "sorclass") {
+ treeCalculators.push_back(new SorClass());
+ }else if (Estimators[i] == "jest") {
+ treeCalculators.push_back(new Jest());
+ }else if (Estimators[i] == "sorest") {
+ treeCalculators.push_back(new SorEst());
+ }else if (Estimators[i] == "thetayc") {
+ treeCalculators.push_back(new ThetaYC());
+ }else if (Estimators[i] == "thetan") {
+ treeCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "morisitahorn") {
+ treeCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ treeCalculators.push_back(new BrayCurtis());
+ }
+ }
}
}
- }
+ }
}
-
- //reset calc for next command
- globaldata->setCalc("");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void TreeGroupCommand::help(){
+ try {
+ mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
+ mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
+ mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision, line and label. You may not use line and label at the same time.\n");
+ mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
+ mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n");
+ mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
+ mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels).\n");
+ mothurOut("Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund).\n");
+ mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ mothurOut("The default value for calc is jclass-thetayc.\n");
+ mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
+ validCalculator->printCalc("treegroup", cout);
+ mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
+ mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "TreeGroupCommand", "help");
exit(1);
- }
+ }
}
+
+
//**********************************************************************************************************************
TreeGroupCommand::~TreeGroupCommand(){
- delete input;
- if (format == "sharedfile") {delete read;}
- else { delete readMatrix; delete matrix; delete list; }
- delete tmap;
+ if (abort == false) {
+
+ if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL;}
+ else { delete readMatrix; delete matrix; delete list; }
+ delete tmap;
+ delete validCalculator;
+ }
}
int TreeGroupCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
if (format == "sharedfile") {
//if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { cout << "You have given no valid calculators." << endl; return 0; }
+ if (treeCalculators.size() == 0) { mothurOut("You have given no valid calculators."); mothurOutEndLine(); return 0; }
//you have groups
read = new ReadOTUFile(globaldata->inputFileName);
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
+ lastLabel = lookup[0]->getLabel();
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0; }
+ if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0; }
+ globaldata->runParse = false;
+
//create tree file
makeSimsShared();
}else{
if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
- if(globaldata->getPrecision() != ""){
- convert(globaldata->getPrecision(), precision);
- }
-
- if(globaldata->getCutOff() != ""){
- convert(globaldata->getCutOff(), cutoff);
- cutoff += (5 / (precision * 10.0));
- }
readMatrix->setCutoff(cutoff);
- if(globaldata->getNameFile() != ""){
- nameMap = new NameAssignment(globaldata->getNameFile());
- nameMap->readMap(1,2);
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
}
else{
nameMap = NULL;
//fills globaldatas tree names
globaldata->Treenames = globaldata->Groups;
-
+
+ globaldata->runParse = false;
+
makeSimsDist();
//create a new filename
outputFile = getRootName(globaldata->inputFileName) + "tre";
createTree();
+ mothurOut("Tree complete. "); mothurOutEndLine();
}
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "createTree");
exit(1);
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "printSims");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
void TreeGroupCommand::makeSimsDist() {
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "makeSimsDist");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
void TreeGroupCommand::makeSimsShared() {
try {
int count = 1;
- EstOutput data;
- vector<SharedRAbundVector*> subset;
- numGroups = globaldata->Groups.size();
-
//clear globaldatas old tree names if any
globaldata->Treenames.clear();
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
- while(lookup[0] != NULL){
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+ set<int> userLines = lines;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
- cout << lookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
+ }
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors();
+ count++;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ needToRun = true;
+ }else {
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
+ }
+ catch(exception& e) {
+ errorOut(e, "TreeGroupCommand", "makeSimsShared");
+ exit(1);
+ }
+}
+
+/***********************************************************/
+void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
+ try{
+ EstOutput data;
+ vector<SharedRAbundVector*> subset;
+ numGroups = thisLookup.size();
//for each calculator
for(int i = 0 ; i < treeCalculators.size(); i++) {
for (int g = 0; g < numGroups; g++) { index[g] = g; }
//create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
+ outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
- for (int k = 0; k < lookup.size(); k++) {
- for (int l = k; l < lookup.size(); l++) {
+ for (int k = 0; k < thisLookup.size(); k++) {
+ for (int l = k; l < thisLookup.size(); l++) {
if (k != l) { //we dont need to similiarity of a groups to itself
//get estimated similarity between 2 groups
subset.clear(); //clear out old pair of sharedrabunds
//add new pair of sharedrabunds
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
+ subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
//save values in similarity matrix
}
}
}
-
+
//creates tree from similarity matrix and write out file
createTree();
}
- }
-
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
- //get next line to process
- lookup = input->getSharedRAbundVectors();
- count++;
- }
-
- for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "TreeGroupCommand", "process");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
/***********************************************************/
+
projects / mothur.git / blobdiff