#include "unifracunweightedcommand.h"
/***********************************************************/
-UnifracUnweightedCommand::UnifracUnweightedCommand() {
+UnifracUnweightedCommand::UnifracUnweightedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+ abort = false;
+ Groups.clear();
- T = globaldata->gTree;
- tmap = globaldata->gTreemap;
- sumFile = globaldata->getTreeFile() + ".uwsummary";
- openOutputFile(sumFile, outSum);
-
- util = new SharedUtil();
- util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze
- util->getCombos(groupComb, globaldata->Groups, numComp);
- globaldata->setGroups("");
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"groups","iters","distance","random"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
- //ABC
- if (numComp != 1) {
- groupComb.push_back(allGroups);
- numComp++;
+ //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; }
+ }
+
+ if (globaldata->gTree.size() == 0) {//no trees were read
+ mothurOut("You must execute the read.tree command, before you may execute the unifrac.unweighted command."); mothurOutEndLine(); abort = true; }
+
+ //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 {
+ splitAtDash(groups, Groups);
+ globaldata->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") { temp = "false"; }
+ phylip = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "true"; }
+ random = isTrue(temp);
+
+ 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";
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ if (abort == false) {
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+ sumFile = globaldata->getTreeFile() + ".uwsummary";
+ openOutputFile(sumFile, outSum);
+
+ util = new SharedUtil();
+ util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, globaldata->Groups, numComp);
+
+ if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
+
+ unweighted = new Unweighted(tmap);
+
+ }
+
}
-
- convert(globaldata->getIters(), iters); //how many random trees to generate
- unweighted = new Unweighted(tmap);
-
}
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";
+ errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
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";
+}
+
+//**********************************************************************************************************************
+
+void UnifracUnweightedCommand::help(){
+ try {
+ mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n");
+ mothurOut("The unifrac.unweighted command parameters are groups, iters, distance and random. No parameters are required.\n");
+ mothurOut("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");
+ mothurOut("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");
+ mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
+ mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
+ mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
+ mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
+ mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
+ mothurOut("The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "UnifracUnweightedCommand", "help");
exit(1);
}
}
+
+
/***********************************************************/
int UnifracUnweightedCommand::execute() {
try {
-
+
+ if (abort == true) { return 0; }
+
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
outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t' << "UWSig" << endl;
- cout << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" << '\t' << "UWSig" << endl;
+ mothurOut("Tree#\tGroups\tUWScore\tUWSig"); mothurOutEndLine();
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
counter = 0;
- unweightedFile = globaldata->getTreeFile() + toString(i+1) + ".unweighted";
- unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
- outSum << i+1 << '\t';
- cout << i+1 << '\t';
+ if (random) { output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".unweighted", itersString); }
//get unweighted for users tree
rscoreFreq.resize(numComp);
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
for (int j = 0; j < iters; j++) {
- //we need a different getValues because when we swap the labels we only want to swap those in each parwise comparison
+ //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], "", "");
-
+
for(int k = 0; k < numComp; k++) {
//add trees unweighted score to map of scores
- it2 = rscoreFreq[k].find(randomData[k]);
- if (it2 != rscoreFreq[k].end()) {//already have that score
+ 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];
}
-
}
- for(int a = 0; a < numComp; a++) {
- 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++) {
- //make rscoreFreq map and rCumul
- 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
+ for(int a = 0; a < numComp; a++) {
+ 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 (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
+ }
+
+ if (random) { UWScoreSig[a].push_back(rCumul[a][userData[a]]); }
+ else { UWScoreSig[a].push_back(0.0); }
}
- UWScoreSig[a].push_back(rCumul[a][userData[a]]);
- }
+ //print output files
+ printUWSummaryFile(i);
+ if (random) { printUnweightedFile(); delete output; }
+ if (phylip) { createPhylipFile(i); }
+
+ rscoreFreq.clear();
+ rCumul.clear();
+ validScores.clear();
+ utreeScores.clear();
+ UWScoreSig.clear();
+ }
-
- printUnweightedFile();
- printUWSummaryFile();
-
- rscoreFreq.clear();
- rCumul.clear();
- validScores.clear();
- utreeScores.clear();
- UWScoreSig.clear();
- }
//reset groups parameter
globaldata->Groups.clear();
outSum.close();
}
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";
+ errorOut(e, "UnifracUnweightedCommand", "execute");
exit(1);
}
}
void UnifracUnweightedCommand::printUnweightedFile() {
try {
vector<double> data;
+ vector<string> tags;
+ tags.push_back("Score");
+ tags.push_back("RandFreq"); tags.push_back("RandCumul");
+
for(int a = 0; a < numComp; a++) {
- initFile(groupComb[a]);
+ output->initFile(groupComb[a], tags);
//print each line
- for (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(data);
+ 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();
}
- resetFile();
+ output->resetFile();
}
-
- out.close();
- inFile.close();
- remove(unweightedFileout.c_str());
-
}
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";
+ errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile");
exit(1);
}
}
/***********************************************************/
-void UnifracUnweightedCommand::printUWSummaryFile() {
+void UnifracUnweightedCommand::printUWSummaryFile(int i) {
try {
//format output
//print each line
for(int a = 0; a < numComp; a++) {
- if (UWScoreSig[a][0] > (1/(float)iters)) {
- outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
- cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
- }else {
- outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
- cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
+ outSum << i+1 << '\t';
+ 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;
+ mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); mothurOutEndLine();
+ }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;
+ mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); mothurOutEndLine();
+ }
+ }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;
+ mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00"); mothurOutEndLine();
}
}
}
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";
+ errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile");
exit(1);
}
}
-/*****************************************************************/
-
-void UnifracUnweightedCommand::initFile(string label){
+/***********************************************************/
+void UnifracUnweightedCommand::createPhylipFile(int i) {
try {
- if(counter != 0){
- openOutputFile(unweightedFileout, out);
- openInputFile(unweightedFile, inFile);
-
- string inputBuffer;
- getline(inFile, inputBuffer);
-
- out << inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
- }else{
- openOutputFile(unweightedFileout, out);
- out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+ string phylipFileName = globaldata->getTreeFile() + toString(i+1) + ".unweighted.dist";
+ ofstream out;
+ openOutputFile(phylipFileName, out);
+
+ //output numSeqs
+ out << globaldata->Groups.size() << endl;
+
+ //make matrix with scores in it
+ vector< vector<float> > dists; dists.resize(globaldata->Groups.size());
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ dists[i].resize(globaldata->Groups.size(), 0.0);
}
-
- out.setf(ios::fixed, ios::floatfield);
- out.setf(ios::showpoint);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void UnifracUnweightedCommand::output(vector<double> data){
- try {
- if(counter != 0){
- string inputBuffer;
- getline(inFile, inputBuffer);
-// out << inputBuffer << setprecision(6) << '\t' << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
- out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
+ //flip it so you can print it
+ int count = 0;
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ for (int l = r+1; l < globaldata->Groups.size(); l++) {
+ dists[r][l] = (1.0 - utreeScores[count][0]);
+ dists[l][r] = (1.0 - utreeScores[count][0]);
+ count++;
+ }
}
- else{
- out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
+
+ //output to file
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ //output name
+ string name = globaldata->Groups[r];
+ 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;
}
-
+ out.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracUnweightedCommand", "createPhylipFile");
exit(1);
}
-};
+}
+/***********************************************************/
-/***********************************************************************/
-void UnifracUnweightedCommand::resetFile(){
- try {
- if(counter != 0){
- out.close();
- inFile.close();
- }
- else{
- out.close();
- }
- counter = 1;
-
- remove(unweightedFile.c_str());
- rename(unweightedFileout.c_str(), unweightedFile.c_str());
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracUnweightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}