else {
//valid paramters for this command
- string Array[] = {"groups","iters"};
+ string Array[] = {"groups","iters","distance","random","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters=parser.getParameters();
- ValidParameters* validParameter = new ValidParameters();
+ ValidParameters validParameter;
//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; }
+ 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
- cout << "You must execute the read.tree command, before you may execute the unifrac.weighted command." << endl; abort = true; }
-
+ mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); mothurOutEndLine(); abort = true; }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- groups = validParameter->validFile(parameters, "groups", false);
+ 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"; }
+ itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
convert(itersString, iters);
- delete validParameter;
+ 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";
+ sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".wsummary";
openOutputFile(sumFile, outSum);
util = new SharedUtil();
}
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";
- 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";
+ errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
exit(1);
}
}
void UnifracWeightedCommand::help(){
try {
- cout << "The unifrac.weighted command can only be executed after a successful read.tree command." << "\n";
- cout << "The unifrac.weighted 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 2 valid groups." << "\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.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters)." << "\n";
- cout << "Example unifrac.weighted(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.weighted command output two files: .weighted and .wsummary their descriptions are in the manual." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "UnifracWeightedCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the UnifracWeightedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
if (abort == true) { return 0; }
Progress* reading;
- reading = new Progress("Comparing to random:", iters);
+ 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...
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
- output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted", itersString);
+ if (random) { output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted", itersString); }
userData = weighted->getValues(T[i]); //userData[0] = weightedscore
//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();
-
- delete output;
-
//clear data
rScores.clear();
uScores.clear();
}
//finish progress bar
- reading->finish();
- delete reading;
+ 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);
}
}
for(int a = 0; a < numComp; 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->output(data);
data.clear();
}
}
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(itersString.length()) << WScoreSig[count] << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.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(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;
+ 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";
+ errorOut(e, "UnifracWeightedCommand", "printWSummaryFile");
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";
+}
+/***********************************************************/
+void UnifracWeightedCommand::createPhylipFile() {
+ try {
+ int count = 0;
+ //for each tree
+ for (int i = 0; i < T.size(); i++) {
+
+ string phylipFileName = outputDir + getSimpleName(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);
+ }
+
+ //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++;
+ }
+ }
+
+ //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) {
+ errorOut(e, "UnifracWeightedCommand", "createPhylipFile");
exit(1);
}
}
-
/***********************************************************/
int UnifracWeightedCommand::findIndex(float score, int index) {
try{
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";
+ 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";
+ errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums");
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);
- }
-
}
/***********************************************************/