#include "unifracunweightedcommand.h"
-/***********************************************************/
-UnifracUnweightedCommand::UnifracUnweightedCommand() {
+//**********************************************************************************************************************
+vector<string> UnifracUnweightedCommand::setParameters(){
try {
- globaldata = GlobalData::getInstance();
-
- T = globaldata->gTree;
- tmap = globaldata->gTreemap;
- unweightedFile = globaldata->getTreeFile() + ".unweighted";
- openOutputFile(unweightedFile, out);
- sumFile = globaldata->getTreeFile() + ".uwsummary";
- openOutputFile(sumFile, outSum);
- distFile = globaldata->getTreeFile() + ".uwdistrib";
- openOutputFile(distFile, outDist);
- setGroups(); //sets users groups to analyze
- convert(globaldata->getIters(), iters); //how many random trees to generate
- unweighted = new Unweighted(tmap);
-
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter prandom("random", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prandom);
+ CommandParameter pdistance("distance", "Multiple", "column-lt-square", "column", "", "", "",false,false); parameters.push_back(pdistance);
+ CommandParameter proot("root", "Boolean", "F", "", "", "", "",false,false); parameters.push_back(proot);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "UnifracUnweightedCommand", "setParameters");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function UnifracUnweightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+string UnifracUnweightedCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The unifrac.unweighted command parameters are tree, group, name, groups, iters, distance, processors, root and random. tree parameter is required unless you have valid current tree file.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n";
+ helpString += "The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n";
+ helpString += "The distance parameter allows you to create a distance file from the results. The default is false. You may set distance to lt, square or column.\n";
+ helpString += "The random parameter allows you to shut off the comparison to random trees. The default is false, meaning compare don't your trees with randomly generated trees.\n";
+ helpString += "The root parameter allows you to include the entire root in your calculations. The default is false, meaning stop at the root for this comparision instead of the root of the entire tree.\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+ helpString += "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n";
+ helpString += "Example unifrac.unweighted(groups=A-B-C, iters=500).\n";
+ helpString += "The default value for groups is all the groups in your groupfile, and iters is 1000.\n";
+ helpString += "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+UnifracUnweightedCommand::UnifracUnweightedCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["unweighted"] = tempOutNames;
+ outputTypes["uwsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
+ exit(1);
+ }
+}
+/***********************************************************/
+UnifracUnweightedCommand::UnifracUnweightedCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ 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; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["unweighted"] = tempOutNames;
+ outputTypes["uwsummary"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("tree");
+ //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["tree"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+ }
+
+ m->runParse = true;
+
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { abort = true; }
+ else if (treefile == "not found") { //if there is a current design file, use it
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ //check for required parameters
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
+ }
+
+ 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") { 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);
+
+ temp = validParameter.validFile(parameters, "root", false); if (temp == "not found") { temp = "F"; }
+ includeRoot = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
+
+ if (!random) { iters = 0; } //turn off random calcs
+
+ //if user selects distance = true and no groups it won't calc the pairwise
+ if ((phylip) && (Groups.size() == 0)) {
+ groups = "all";
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
exit(1);
}
}
+
/***********************************************************/
int UnifracUnweightedCommand::execute() {
try {
- //get unweighted for users tree
- userData.resize(1,0); //data[0] = unweightedscore
- randomData.resize(1,0); //data[0] = unweightedscore
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ if (groupfile != "") {
+ //read in group map info.
+ tmap = new TreeMap(groupfile);
+ tmap->readMap();
+ }else{ //fake out by putting everyone in one group
+ Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
+ tmap = new TreeMap();
+
+ for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
+ }
+
+ if (namefile != "") { readNamesFile(); }
+
+ read = new ReadNewickTree(treefile);
+ int readOk = read->read(tmap);
+
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
+
+ read->AssembleTrees();
+ T = read->getTrees();
+ delete read;
+
+ //make sure all files match
+ //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
+ int numNamesInTree;
+ if (namefile != "") {
+ if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
+ else { numNamesInTree = m->Treenames.size(); }
+ }else { numNamesInTree = m->Treenames.size(); }
- //format output
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
- outDist << "Groups Used ";
- for (int m = 0; m < globaldata->Groups.size(); m++) {
- outDist << globaldata->Groups[m] << " ";
+ //output any names that are in group file but not in tree
+ if (numNamesInTree < tmap->getNumSeqs()) {
+ for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
+ //is that name in the tree?
+ int count = 0;
+ for (int j = 0; j < m->Treenames.size(); j++) {
+ if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
+ count++;
+ }
+
+ if (m->control_pressed) {
+ delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ m->Groups.clear();
+ return 0;
+ }
+
+ //then you did not find it so report it
+ if (count == m->Treenames.size()) {
+ //if it is in your namefile then don't remove
+ map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
+
+ if (it == nameMap.end()) {
+ m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
+ tmap->removeSeq(tmap->namesOfSeqs[i]);
+ i--; //need this because removeSeq removes name from namesOfSeqs
+ }
+ }
+ }
}
- outDist << endl;
+
+ sumFile = outputDir + m->getSimpleName(treefile) + ".uwsummary";
+ outputNames.push_back(sumFile); outputTypes["uwsummary"].push_back(sumFile);
+ m->openOutputFile(sumFile, outSum);
+
+ util = new SharedUtil();
+ util->setGroups(m->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, m->Groups, numComp);
+ delete util;
+
+ if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+
+ unweighted = new Unweighted(tmap, includeRoot);
- outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl;
+ int start = time(NULL);
+ userData.resize(numComp,0); //data[0] = unweightedscore
+ randomData.resize(numComp,0); //data[0] = unweightedscore
//create new tree with same num nodes and leaves as users
- randT = new Tree();
-
+
+ if (numComp < processors) { processors = numComp; }
+
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t' << "UWSig" << endl;
+ m->mothurOut("Tree#\tGroups\tUWScore\tUWSig"); m->mothurOutEndLine();
+
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
- cout << "Processing tree " << i+1 << endl;
- userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore
+ if (m->control_pressed) {
+ delete tmap; delete unweighted;
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
+ outSum.close();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
- //update uscoreFreq
- it = uscoreFreq.find(userData[0]);
- if (it == uscoreFreq.end()) {//new score
- uscoreFreq[userData[0]] = 1;
- }else{ uscoreFreq[userData[0]]++; }
+ counter = 0;
- //add users score to valid scores
- validScores[userData[0]] = userData[0];
+ if (random) {
+ output = new ColumnFile(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted", itersString);
+ outputNames.push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted");
+ outputTypes["unweighted"].push_back(outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted");
+ }
- //saves users score
- utreeScores.push_back(userData[0]);
- //copy T[i]'s info.
- randT->getCopy(T[i]);
+ //get unweighted for users tree
+ rscoreFreq.resize(numComp);
+ rCumul.resize(numComp);
+ utreeScores.resize(numComp);
+ UWScoreSig.resize(numComp);
+
+ userData = unweighted->getValues(T[i], processors, outputDir); //userData[0] = unweightedscore
+
+ if (m->control_pressed) { delete tmap; delete unweighted;
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }return 0; }
- //get unweighted scores for random trees
+ //output scores for each combination
+ for(int k = 0; k < numComp; k++) {
+ //saves users score
+ utreeScores[k].push_back(userData[k]);
+
+ //add users score to validscores
+ validScores[userData[k]] = userData[k];
+ }
+
+ //get unweighted scores for random trees - if random is false iters = 0
for (int j = 0; j < iters; j++) {
- //create a random tree with same topology as T[i], but different labels
- randT->assembleRandomUnifracTree();
- //get pscore of random tree
- randomData = unweighted->getValues(randT);
-
- //add trees unweighted score to map of scores
- it2 = rscoreFreq.find(randomData[0]);
- if (it2 != rscoreFreq.end()) {//already have that score
- rscoreFreq[randomData[0]]++;
- }else{//first time we have seen this score
- rscoreFreq[randomData[0]] = 1;
- }
+
+ //we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
+ randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
+ if (m->control_pressed) { delete tmap; delete unweighted;
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ for(int k = 0; k < numComp; k++) {
+ //add trees unweighted score to map of scores
+ map<float,float>::iterator it = rscoreFreq[k].find(randomData[k]);
+ if (it != rscoreFreq[k].end()) {//already have that score
+ rscoreFreq[k][randomData[k]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[k][randomData[k]] = 1;
+ }
+
+ //add randoms score to validscores
+ validScores[randomData[k]] = randomData[k];
+ }
- //output info to uwdistrib file
- outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << randomData[0] << endl;
+ //report progress
+// m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
}
-
- saveRandomScores(); //save all random scores for unweighted file
-
- //find the signifigance of the score
- float rcumul = 1.0000;
- for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
- rCumul[it->first] = rcumul;
- //get percentage of random trees with that info
- rscoreFreq[it->first] /= iters;
- rcumul-= it->second;
+
+ for(int a = 0; a < numComp; a++) {
+ float rcumul = 1.0000;
+
+ if (random) {
+ //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
+ for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
+ //make rscoreFreq map and rCumul
+ map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
+ rCumul[a][it->first] = rcumul;
+ //get percentage of random trees with that info
+ if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul-= it2->second; }
+ else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
+ }
+ UWScoreSig[a].push_back(rCumul[a][userData[a]]);
+ }else { UWScoreSig[a].push_back(0.0); }
+
}
- //save the signifigance of the users score for printing later
- UWScoreSig.push_back(rCumul[userData[0]]);
+ if (m->control_pressed) { delete tmap; delete unweighted;
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ //print output files
+ printUWSummaryFile(i);
+ if (random) { printUnweightedFile(); delete output; }
+ if (phylip) { createPhylipFile(i); }
- //clear random data
- rscoreFreq.clear(); //you clear this because in the summary file you want the unweighted signifinance to be relative to these 1000 trees.
- rCumul.clear();
+ rscoreFreq.clear();
+ rCumul.clear();
+ validScores.clear();
+ utreeScores.clear();
+ UWScoreSig.clear();
}
- float ucumul = 1.0000;
- float rcumul = 1.0000;
- //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
- for (it = validScores.begin(); it != validScores.end(); it++) {
- it2 = uscoreFreq.find(it->first);
- //make uCumul map
- uCumul[it->first] = ucumul;
- //user data has that score
- if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul-= it2->second; }
- else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
-
- //make rscoreFreq map and rCumul
- it2 = totalrscoreFreq.find(it->first);
- rCumul[it->first] = rcumul;
- //get percentage of random trees with that info
- if (it2 != totalrscoreFreq.end()) { totalrscoreFreq[it->first] /= (iters*T.size()); rcumul-= it2->second; }
- else { totalrscoreFreq[it->first] = 0.0000; } //no random trees with that score
-
- }
+
+ outSum.close();
+ m->Groups.clear();
+ delete tmap; delete unweighted;
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
- printUnweightedFile();
- printUWSummaryFile();
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
- //reset groups parameter
- globaldata->Groups.clear();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine();
- delete randT;
+ //set phylip file as new current phylipfile
+ string current = "";
+ itTypes = outputTypes.find("phylip");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+ }
+
+ //set column file as new current columnfile
+ itTypes = outputTypes.find("column");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "UnifracUnweightedCommand", "execute");
exit(1);
}
}
/***********************************************************/
void UnifracUnweightedCommand::printUnweightedFile() {
try {
- //column headers
+ vector<double> data;
+ vector<string> tags;
- out << "Groups Used ";
- for (int m = 0; m < globaldata->Groups.size(); m++) {
- out << globaldata->Groups[m] << " ";
+ tags.push_back("Score");
+ tags.push_back("RandFreq"); tags.push_back("RandCumul");
+
+ for(int a = 0; a < numComp; a++) {
+ output->initFile(groupComb[a], tags);
+ //print each line
+ for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
+ data.push_back(it->first); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
+ output->output(data);
+ data.clear();
+ }
+ output->resetFile();
}
- out << endl;
-
- out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
-
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- //print each line
- for (it = validScores.begin(); it != validScores.end(); it++) {
- out << setprecision(6) << it->first << '\t' << '\t' << uscoreFreq[it->first] << '\t' << uCumul[it->first] << '\t' << totalrscoreFreq[it->first] << '\t' << rCumul[it->first] << endl;
- }
-
- out.close();
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUnweightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile");
exit(1);
}
}
/***********************************************************/
-void UnifracUnweightedCommand::printUWSummaryFile() {
+void UnifracUnweightedCommand::printUWSummaryFile(int i) {
try {
- //column headers
-
- outSum << "Groups Used ";
- for (int m = 0; m < globaldata->Groups.size(); m++) {
- outSum << globaldata->Groups[m] << " ";
- }
- outSum << endl;
-
- outSum << "Tree#" << '\t' << "UWScore" << '\t' << '\t' << "UWSig" << endl;
-
+
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
-
+
//print each line
- for (int i = 0; i< T.size(); i++) {
- outSum << setprecision(6) << i+1 << '\t' << '\t' << utreeScores[i] << '\t' << UWScoreSig[i] << endl;
+
+ for(int a = 0; a < numComp; a++) {
+ outSum << i+1 << '\t';
+ m->mothurOut(toString(i+1) + "\t");
+
+ if (random) {
+ if (UWScoreSig[a][0] > (1/(float)iters)) {
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])+ "\n");
+ }else {
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters))) + "\n");
+ }
+ }else{
+ outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
+ cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00\n");
+ }
}
- outSum.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function printUWSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile");
exit(1);
}
}
/***********************************************************/
-void UnifracUnweightedCommand::saveRandomScores() {
+void UnifracUnweightedCommand::createPhylipFile(int i) {
try {
- for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
- //does this score already exist in the total map
- it2 = totalrscoreFreq.find(it->first);
- //if yes then add them
- if (it2 != totalrscoreFreq.end()) {
- totalrscoreFreq[it->first] += rscoreFreq[it->first];
- }else{ //its a new score
- totalrscoreFreq[it->first] = rscoreFreq[it->first];
+ string phylipFileName;
+ if ((outputForm == "lt") || (outputForm == "square")) {
+ phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.phylip.dist";
+ outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName);
+ }else { //column
+ phylipFileName = outputDir + m->getSimpleName(treefile) + toString(i+1) + ".unweighted.column.dist";
+ outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName);
+ }
+
+ ofstream out;
+ m->openOutputFile(phylipFileName, out);
+
+ if ((outputForm == "lt") || (outputForm == "square")) {
+ //output numSeqs
+ out << m->Groups.size() << endl;
+ }
+
+ //make matrix with scores in it
+ vector< vector<float> > dists; dists.resize(m->Groups.size());
+ for (int i = 0; i < m->Groups.size(); i++) {
+ dists[i].resize(m->Groups.size(), 0.0);
+ }
+
+ //flip it so you can print it
+ int count = 0;
+ for (int r=0; r<m->Groups.size(); r++) {
+ for (int l = 0; l < r; l++) {
+ dists[r][l] = utreeScores[count][0];
+ dists[l][r] = utreeScores[count][0];
+ count++;
}
}
+
+ //output to file
+ for (int r=0; r<m->Groups.size(); r++) {
+ //output name
+ string name = m->Groups[r];
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+
+ 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 < m->Groups.size(); l++) { out << dists[r][l] << '\t'; }
+ out << endl;
+ }else{
+ //output distances
+ for (int l = 0; l < r; l++) {
+ string otherName = m->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();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "UnifracUnweightedCommand", "createPhylipFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function saveRandomScores. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************/
-
-void UnifracUnweightedCommand::setGroups() {
+}/*****************************************************************/
+int UnifracUnweightedCommand::readNamesFile() {
try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- //check that groups are valid
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
- cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
- // erase the invalid group from globaldata->Groups
- globaldata->Groups.erase (globaldata->Groups.begin()+i);
- }
- }
+ m->names.clear();
+ numUniquesInName = 0;
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string first, second;
+ map<string, string>::iterator itNames;
+
+ while(!in.eof()) {
+ in >> first >> second; m->gobble(in);
+
+ numUniquesInName++;
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ itNames = m->names.find(first);
+ if (itNames == m->names.end()) {
+ m->names[first] = second;
+
+ //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
+ vector<string> dupNames;
+ m->splitAtComma(second, dupNames);
+
+ for (int i = 0; i < dupNames.size(); i++) {
+ nameMap[dupNames[i]] = dupNames[i];
+ if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
}
- }
-
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
+ }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
}
+ in.close();
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "UnifracUnweightedCommand", "readNamesFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
-/*****************************************************************/
+/***********************************************************/
+
+
+
projects / mothur.git / blobdiff