#include "unifracweightedcommand.h"
/***********************************************************/
-UnifracWeightedCommand::UnifracWeightedCommand() {
+UnifracWeightedCommand::UnifracWeightedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+ abort = false;
+ Groups.clear();
- T = globaldata->gTree;
- tmap = globaldata->gTreemap;
- sumFile = globaldata->getTreeFile() + ".wsummary";
- openOutputFile(sumFile, outSum);
+ //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;
+
+ //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.weighted 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;
+ }
- setGroups(); //sets the groups the user wants to analyze
- convert(globaldata->getIters(), iters); //how many random trees to generate
- weighted = new Weighted(tmap);
+ 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 (abort == false) {
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+ sumFile = globaldata->getTreeFile() + ".wsummary";
+ openOutputFile(sumFile, outSum);
+
+ util = new SharedUtil();
+ string s; //to make work with setgroups
+ util->setGroups(globaldata->Groups, tmap->namesOfGroups, s, numGroups, "weighted"); //sets the groups the user wants to analyze
+ util->getCombos(groupComb, globaldata->Groups, numComp);
+
+ weighted = new Weighted(tmap);
+
+ }
+ }
+
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function UnifracWeightedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void UnifracWeightedCommand::help(){
+ try {
+ mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n");
+ mothurOut("The unifrac.weighted 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 2 valid groups.\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.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n");
+ mothurOut("Example unifrac.weighted(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.weighted command output two files: .weighted and .wsummary 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, "UnifracWeightedCommand", "help");
exit(1);
}
}
+
/***********************************************************/
int UnifracWeightedCommand::execute() {
try {
+
+ if (abort == true) { return 0; }
+
+ Progress* reading;
+ if (random) { reading = new Progress("Comparing to random:", iters); }
//get weighted for users tree
userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
counter = 0;
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
- weightedFile = globaldata->getTreeFile() + toString(i+1) + ".weighted";
- weightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".weighted";
+
+ if (random) { output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted", itersString); }
userData = weighted->getValues(T[i]); //userData[0] = weightedscore
count++;
}
}
+
+ //update progress bar
+ reading->update(j);
+
}
//removeValidScoresDuplicates();
//find the signifigance of the score for summary file
- for (int f = 0; f < numComp; f++) {
- //sort random scores
- sort(rScores[f].begin(), rScores[f].end());
+ if (random) {
+ for (int f = 0; f < numComp; f++) {
+ //sort random scores
+ sort(rScores[f].begin(), rScores[f].end());
+
+ //the index of the score higher than yours is returned
+ //so if you have 1000 random trees the index returned is 100
+ //then there are 900 trees with a score greater then you.
+ //giving you a signifigance of 0.900
+ int index = findIndex(userData[f], f); if (index == -1) { mothurOut("error in UnifracWeightedCommand"); mothurOutEndLine(); exit(1); } //error code
+
+ //the signifigance is the number of trees with the users score or higher
+ WScoreSig.push_back((iters-index)/(float)iters);
+ }
- //the index of the score higher than yours is returned
- //so if you have 1000 random trees the index returned is 100
- //then there are 900 trees with a score greater then you.
- //giving you a signifigance of 0.900
- int index = findIndex(userData[f], f); if (index == -1) { cout << "error in UnifracWeightedCommand" << endl; exit(1); } //error code
-
- //the signifigance is the number of trees with the users score or higher
- WScoreSig.push_back((iters-index)/(float)iters);
+ //out << "Tree# " << i << endl;
+ calculateFreqsCumuls();
+ printWeightedFile();
+
+ delete output;
}
- //out << "Tree# " << i << endl;
- calculateFreqsCumuls();
- printWeightedFile();
-
//clear data
rScores.clear();
uScores.clear();
validScores.clear();
}
+ //finish progress bar
+ if (random) { reading->finish(); delete reading; }
+
printWSummaryFile();
+ if (phylip) { createPhylipFile(); }
+
//clear out users groups
globaldata->Groups.clear();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "execute");
exit(1);
}
}
void UnifracWeightedCommand::printWeightedFile() {
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++) {
+ 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(data);
+ output->output(data);
data.clear();
}
- resetFile();
+ output->resetFile();
}
-
- out.close();
- inFile.close();
- remove(weightedFileout.c_str());
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "printWeightedFile");
exit(1);
}
}
try {
//column headers
outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl;
- cout << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl;
+ mothurOut("Tree#\tGroups\tWScore\tWSig"); mothurOutEndLine();
//format output
outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
int count = 0;
for (int i = 0; i < T.size(); i++) {
for (int j = 0; j < numComp; j++) {
- if (WScoreSig[count] > (1/(float)iters)) {
- outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << WScoreSig[count] << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << WScoreSig[count] << endl;
+ if (random) {
+ if (WScoreSig[count] > (1/(float)iters)) {
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
+ mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); mothurOutEndLine();
+ }else{
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
+ mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); mothurOutEndLine();
+ }
}else{
- outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
+ mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); mothurOutEndLine();
}
count++;
}
outSum.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function printWeightedFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "printWSummaryFile");
exit(1);
}
}
-
/***********************************************************/
-int UnifracWeightedCommand::findIndex(float score, int index) {
- try{
- for (int i = 0; i < rScores[index].size(); i++) {
- if (rScores[index][i] >= score) { return i; }
- }
- return rScores[index].size();
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function findIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************/
-void UnifracWeightedCommand::setGroups() {
+void UnifracWeightedCommand::createPhylipFile() {
try {
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ int count = 0;
+ //for each tree
+ for (int i = 0; i < T.size(); i++) {
+
+ string phylipFileName = globaldata->getTreeFile() + toString(i+1) + ".weighted.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);
}
- }else {
- if (globaldata->getGroups() != "all") {
- //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);
- }
- }
- //if the user only entered invalid groups
- if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- }else if (globaldata->Groups.size() == 1) {
- cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- numGroups = tmap->getNumGroups();
- globaldata->Groups.clear();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- }
- }else { numGroups = globaldata->Groups.size(); }
- }else { //users wants all groups
- numGroups = tmap->getNumGroups();
- globaldata->Groups.clear();
- globaldata->setGroups("");
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ //flip it so you can print it
+ 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]);
+ dists[l][r] = (1.0 - utreeScores[count]);
+ count++;
}
}
- }
-
- //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
- numComp = 0;
- for (int i=0; i<numGroups; i++) {
- numComp += i;
- for (int l = i+1; l < numGroups; l++) {
- //set group comparison labels
- groupComb.push_back(globaldata->Groups[i] + "-" + globaldata->Groups[l]);
+
+ //output to file
+ for (int r=0; r<globaldata->Groups.size(); r++) {
+ //output name
+ out << globaldata->Groups[r] << '\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 UnifracWeightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "createPhylipFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************/
+int UnifracWeightedCommand::findIndex(float score, int index) {
+ try{
+ for (int i = 0; i < rScores[index].size(); i++) {
+ if (rScores[index][i] >= score) { return i; }
+ }
+ return rScores[index].size();
+ }
+ catch(exception& e) {
+ errorOut(e, "UnifracWeightedCommand", "findIndex");
exit(1);
}
}
for (int f = 0; f < numComp; f++) {
for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7... you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3...
validScores[rScores[f][i]] = rScores[f][i];
- it = rScoreFreq[f].find(rScores[f][i]);
+ map<float,float>::iterator it = rScoreFreq[f].find(rScores[f][i]);
if (it != rScoreFreq[f].end()) {
rScoreFreq[f][rScores[f][i]]++;
}else{
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++) {
+ for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
//make rscoreFreq map and rCumul
- it2 = rScoreFreq[a].find(it->first);
+ 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; }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function calculateFreqsCums. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-
-/*****************************************************************/
-
-void UnifracWeightedCommand::initFile(string label){
- try {
- if(counter != 0){
- openOutputFile(weightedFileout, out);
- openInputFile(weightedFile, inFile);
-
- string inputBuffer;
- getline(inFile, inputBuffer);
-
- out << inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
- }else{
- openOutputFile(weightedFileout, out);
- out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
- }
-
- out.setf(ios::fixed, ios::floatfield);
- out.setf(ios::showpoint);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums");
exit(1);
}
}
-/***********************************************************************/
+/***********************************************************/
-void UnifracWeightedCommand::output(vector<double> data){
- try {
- if(counter != 0){
- string inputBuffer;
- getline(inFile, inputBuffer);
- out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
- }
- else{
- out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-};
-/***********************************************************************/
-
-void UnifracWeightedCommand::resetFile(){
- try {
- if(counter != 0){
- out.close();
- inFile.close();
- }
- else{
- out.close();
- }
- counter = 1;
-
- remove(weightedFile.c_str());
- rename(weightedFileout.c_str(), weightedFile.c_str());
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
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