#include "unifracunweightedcommand.h"
/***********************************************************/
-UnifracUnweightedCommand::UnifracUnweightedCommand() {
+UnifracUnweightedCommand::UnifracUnweightedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+ abort = false;
+ Groups.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"groups","iters"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //check to make sure all parameters are valid for command
+ for (it4 = parameters.begin(); it4 != parameters.end(); it4++) {
+ if (validParameter->isValidParameter(it4->first, myArray, it4->second) != true) { abort = true; }
+ }
+
+ if (globaldata->gTree.size() == 0) {//no trees were read
+ cout << "You must execute the read.tree command, before you may execute the unifrac.unweighted command." << endl; 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);
+
+ delete validParameter;
+
+ 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);
+
+ }
+
+ }
- 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);
-
- 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";
exit(1);
}
}
+
+//**********************************************************************************************************************
+
+void UnifracUnweightedCommand::help(){
+ try {
+ cout << "The unifrac.unweighted command can only be executed after a successful read.tree command." << "\n";
+ cout << "The unifrac.unweighted command parameters are groups and iters. No parameters are required." << "\n";
+ cout << "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";
+ cout << "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";
+ cout << "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters)." << "\n";
+ cout << "Example unifrac.unweighted(groups=A-B-C, iters=500)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile, and iters is 1000." << "\n";
+ cout << "The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the UnifracUnweightedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the UnifracUnweightedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ 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
-
- //format output
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
- outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl;
+ 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
- randT = new Tree();
-
+
+ outSum << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" <<'\t' << "UWSig" << endl;
+ cout << "Tree#" << '\t' << "Groups" << '\t' << "UWScore" << '\t' << "UWSig" << endl;
+
//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
+ counter = 0;
- //update uscoreFreq
- it = uscoreFreq.find(userData[0]);
- if (it == uscoreFreq.end()) {//new score
- uscoreFreq[userData[0]] = 1;
- }else{ uscoreFreq[userData[0]]++; }
+ output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".unweighted", itersString);
- //add users score to valid scores
- validScores[userData[0]] = userData[0];
-
- //saves users score
- utreeScores.push_back(userData[0]);
+ //get unweighted for users tree
+ rscoreFreq.resize(numComp);
+ rCumul.resize(numComp);
+ utreeScores.resize(numComp);
+ UWScoreSig.resize(numComp);
+
+ userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore
- //copy T[i]'s info.
- randT->getCopy(T[i]);
+ //output scores for each combination
+ for(int k = 0; k < numComp; k++) {
+ //saves users score
+ utreeScores[k].push_back(userData[k]);
+
+ }
//get unweighted scores for random trees
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 parwise 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
+ rscoreFreq[k][randomData[k]]++;
+ }else{//first time we have seen this score
+ rscoreFreq[k][randomData[k]] = 1;
+ }
- //add randoms score to validscores
- validScores[randomData[0]] = randomData[0];
+ //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;
}
-
- //find the signifigance of the score
- float rcumul = 0.0000;
- for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) {
- //get percentage of random trees with that info
- rscoreFreq[it->first] /= iters;
- rcumul+= it->second;
- rCumul[it->first] = rcumul;
+
+ 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
+ }
+ UWScoreSig[a].push_back(rCumul[a][userData[a]]);
}
-
- //save the signifigance of the users score for printing later
- UWScoreSig.push_back(rCumul[userData[0]]);
-
- saveRandomScores(); //save all random scores for unweighted file
- //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();
- }
- float ucumul = 0.0000;
- float rcumul = 0.0000;
- //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);
- //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 uCumul map
- uCumul[it->first] = ucumul;
+
+ printUnweightedFile();
+ printUWSummaryFile(i);
- //make rscoreFreq map and rCumul
- it2 = totalrscoreFreq.find(it->first);
- //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
- rCumul[it->first] = rcumul;
+ delete output;
+ rscoreFreq.clear();
+ rCumul.clear();
+ validScores.clear();
+ utreeScores.clear();
+ UWScoreSig.clear();
}
- printUnweightedFile();
- printUWSummaryFile();
-
- //reset randomTree parameter to 0
- globaldata->setRandomTree("0");
-
- delete randT;
+ //reset groups parameter
+ globaldata->Groups.clear();
+ outSum.close();
return 0;
/***********************************************************/
void UnifracUnweightedCommand::printUnweightedFile() {
try {
- //column headers
-
- 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();
+ 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++) {
+ 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->output(data);
+ data.clear();
+ }
+ output->resetFile();
+ }
}
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";
}
/***********************************************************/
-void UnifracUnweightedCommand::printUWSummaryFile() {
+void UnifracUnweightedCommand::printUWSummaryFile(int i) {
try {
- //column headers
- 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';
+ cout << i+1 << '\t';
+
+ 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;
+ }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;
+ }
}
- 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);
}
}
+
/***********************************************************/
-void UnifracUnweightedCommand::saveRandomScores() {
- try {
- //update total map with new random scores
- 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()) {
- it2->second += it->second;
- }else{ //its a new score
- totalrscoreFreq[it->first] = 1;
- }
- }
- }
- 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";
- 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);
- }
-}
-/***********************************************************/
\ No newline at end of file
+
projects / mothur.git / blobdiff