#include "parsimonycommand.h"
/***********************************************************/
-ParsimonyCommand::ParsimonyCommand() {
+ParsimonyCommand::ParsimonyCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+ abort = false;
+ Groups.clear();
- //randomtree will tell us if user had their own treefile or if they just want the random distribution
- randomtree = globaldata->getRandomTree();
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- //user has entered their own tree
- if (randomtree == "") {
- T = globaldata->gTree;
- tmap = globaldata->gTreemap;
- parsFile = globaldata->getTreeFile() + ".parsimony";
- parsFileout = globaldata->getTreeFile() + "temp" + ".parsimony";
- sumFile = globaldata->getTreeFile() + ".psummary";
- openOutputFile(sumFile, outSum);
- }else { //user wants random distribution
- savetmap = globaldata->gTreemap;
- getUserInput();
- parsFile = randomtree;
- parsFileout = globaldata->getTreeFile() + "temp";
- }
+ else {
+ //valid paramters for this command
+ string Array[] = {"random","groups","iters"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
- //set users groups to analyze
- setGroups();
- convert(globaldata->getIters(), iters); //how many random trees to generate
- pars = new Parsimony(tmap);
- counter = 0;
+ //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; }
+ }
+
+ randomtree = validParameter.validFile(parameters, "random", false); if (randomtree == "not found") { randomtree = ""; }
+
+ //are you trying to use parsimony without reading a tree or saying you want random distribution
+ if (randomtree == "") {
+ if (globaldata->gTree.size() == 0) {
+ cout << "You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony 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);
+
+ if (abort == false) {
+ //randomtree will tell us if user had their own treefile or if they just want the random distribution
+ //user has entered their own tree
+ if (randomtree == "") {
+ T = globaldata->gTree;
+ tmap = globaldata->gTreemap;
+ output = new ColumnFile(globaldata->getTreeFile() + ".parsimony", itersString);
+ sumFile = globaldata->getTreeFile() + ".psummary";
+ openOutputFile(sumFile, outSum);
+ }else { //user wants random distribution
+ savetmap = globaldata->gTreemap;
+ getUserInput();
+ output = new ColumnFile(randomtree, itersString);
+ }
+
+ //set users groups to analyze
+ 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); }
+
+ pars = new Parsimony(tmap);
+ counter = 0;
+
+ }
+
+ }
}
catch(exception& e) {
exit(1);
}
}
+
+//**********************************************************************************************************************
+
+void ParsimonyCommand::help(){
+ try {
+ cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
+ cout << "The parsimony command parameters are random, 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 parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters)." << "\n";
+ cout << "Example parsimony(random=out, iters=500)." << "\n";
+ cout << "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony)," << "\n";
+ cout << "and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ParsimonyCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
/***********************************************************/
int ParsimonyCommand::execute() {
try {
+ if (abort == true) { return 0; }
+
+ Progress* reading;
+ reading = new Progress("Comparing to random:", iters);
+
//get pscore for users tree
userData.resize(numComp,0); //data = AB, AC, BC, ABC.
randomData.resize(numComp,0); //data = AB, AC, BC, ABC.
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC.
-
+
//output scores for each combination
for(int k = 0; k < numComp; k++) {
+
//update uscoreFreq
- it = uscoreFreq[k].find(userData[k]);
+ map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
if (it == uscoreFreq[k].end()) {//new score
uscoreFreq[k][userData[k]] = 1;
}else{ uscoreFreq[k][userData[k]]++; }
for (int j = 0; j < iters; j++) {
//create new tree with same num nodes and leaves as users
randT = new Tree();
+
//create random relationships between nodes
randT->assembleRandomTree();
+
//get pscore of random tree
randomData = pars->getValues(randT);
-
+
for(int r = 0; r < numComp; r++) {
//add trees pscore to map of scores
- it2 = rscoreFreq[r].find(randomData[r]);
- if (it2 != rscoreFreq[r].end()) {//already have that score
+ map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
+ if (it != rscoreFreq[r].end()) {//already have that score
rscoreFreq[r][randomData[r]]++;
}else{//first time we have seen this score
rscoreFreq[r][randomData[r]] = 1;
validScores[randomData[r]] = randomData[r];
}
+ //update progress bar
+ reading->update(j);
+
delete randT;
}
+
}else {
//get pscores for random trees
for (int j = 0; j < iters; j++) {
//create new tree with same num nodes and leaves as users
randT = new Tree();
//create random relationships between nodes
+
randT->assembleRandomTree();
+
//get pscore of random tree
randomData = pars->getValues(randT);
-
+
for(int r = 0; r < numComp; r++) {
//add trees pscore to map of scores
- it2 = rscoreFreq[r].find(randomData[r]);
- if (it2 != rscoreFreq[r].end()) {//already have that score
+ map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
+ if (it != rscoreFreq[r].end()) {//already have that score
rscoreFreq[r][randomData[r]]++;
}else{//first time we have seen this score
rscoreFreq[r][randomData[r]] = 1;
validScores[randomData[r]] = randomData[r];
}
+ //update progress bar
+ reading->update(j);
+
delete randT;
}
}
-
+
for(int a = 0; a < numComp; a++) {
float rcumul = 0.0000;
float ucumul = 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++) {
+ for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
if (randomtree == "") {
- it2 = uscoreFreq[a].find(it->first);
+ map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
//user data has that score
if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second; }
else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
}
//make rscoreFreq map and rCumul
- it2 = rscoreFreq[a].find(it->first);
+ map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
//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
}
}
+ //finish progress bar
+ reading->finish();
+ delete reading;
+
+
printParsimonyFile();
if (randomtree == "") { printUSummaryFile(); }
//reset globaldata's treemap if you just did random distrib
- if (randomtree != "") { globaldata->gTreemap = savetmap; }
+ if (randomtree != "") {
+ //memory leak prevention
+ //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
+ globaldata->gTreemap = savetmap;
+ }
- //reset randomTree parameter to ""
- globaldata->setRandomTree("");
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
return 0;
void ParsimonyCommand::printParsimonyFile() {
try {
vector<double> data;
+ vector<string> tags;
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ if (randomtree == "") {
+ tags.push_back("Score"); tags.push_back("UserFreq"); tags.push_back("UserCumul"); tags.push_back("RandFreq"); tags.push_back("RandCumul");
+ }else {
+ 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<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
if (randomtree == "") {
data.push_back(it->first); data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
}else{
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(parsFileout.c_str());
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
for (int i = 0; i< T.size(); i++) {
for(int a = 0; a < numComp; a++) {
if (UScoreSig[a][i] > (1/(float)iters)) {
- outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << UScoreSig[a][i] << endl;
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << UScoreSig[a][i] << endl;
}else {
- outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl;
- cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(globaldata->getIters().length()) << '\t' << "<" << (1/float(iters)) << endl;
+ outSum << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
+ cout << setprecision(6) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << setprecision(itersString.length()) << '\t' << "<" << (1/float(iters)) << endl;
}
}
}
getline(cin, s);
//save tmap for later
+ //memory leak prevention
+ //if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
globaldata->gTreemap = tmap;
+ globaldata->Treenames = tmap->namesOfSeqs;
}
catch(exception& e) {
exit(1);
}
}
-/***********************************************************/
-
-void ParsimonyCommand::setGroups() {
- try {
- string allGroups = "";
- numGroups = 0;
- //if the user has not entered specific groups to analyze then do them all
- if (globaldata->Groups.size() != 0) {
- if (globaldata->Groups[0] != "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) {
- 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]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i] + "-";
- }
- allGroups = allGroups.substr(0, allGroups.length()-1);
- }else {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- allGroups += globaldata->Groups[i] + "-";
- numGroups++;
- }
- allGroups = allGroups.substr(0, allGroups.length()-1);
- }
- }else{//user has enter "all" and wants the default groups
- globaldata->Groups.clear();
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i] + "-";
- }
- allGroups = allGroups.substr(0, allGroups.length()-1);
- globaldata->setGroups("");
- }
- }else {
- for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- allGroups += tmap->namesOfGroups[i] + "-";
- }
- allGroups = allGroups.substr(0, allGroups.length()-1);
- numGroups = 1;
- }
-
- //calculate number of comparsions
- numComp = 0;
- for (int r=0; r<numGroups; r++) {
- for (int l = r+1; l < numGroups; l++) {
- groupComb.push_back(globaldata->Groups[r]+ "-" +globaldata->Groups[l]);
- numComp++;
- }
- }
-
- //ABC
- if (numComp != 1) {
- groupComb.push_back(allGroups);
- numComp++;
- }
-
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
-}
-/*****************************************************************/
-
-void ParsimonyCommand::initFile(string label){
- try {
- if(counter != 0){
- openOutputFile(parsFileout, out);
- openInputFile(parsFile, inFile);
-
- string inputBuffer;
- getline(inFile, inputBuffer);
-
- if (randomtree == "") {
- out << inputBuffer << '\t' << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
- }else {
- out << inputBuffer << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
- }
- }else{
- openOutputFile(parsFileout, out);
- //column headers
- if (randomtree == "") {
- out << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
- }else {
- out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
- }
- }
-
- out.setf(ios::fixed, ios::floatfield);
- out.setf(ios::showpoint);
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function initFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************************/
-void ParsimonyCommand::output(vector<double> data){
- try {
- if(counter != 0){
- string inputBuffer;
- getline(inFile, inputBuffer);
-
- if (randomtree == "") {
- out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << endl;
- }else{
- out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
- }
- }
- else{
- if (randomtree == "") {
- out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << '\t' << data[3] << '\t' << data[4] << 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 ParsimonyCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-void ParsimonyCommand::resetFile(){
- try {
- if(counter != 0){
- out.close();
- inFile.close();
- }
- else{
- out.close();
- }
- counter = 1;
-
- remove(parsFile.c_str());
- rename(parsFileout.c_str(), parsFile.c_str());
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ParsimonyCommand class function resetFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
+/***********************************************************/
projects / mothur.git / blobdiff