X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=da997c13b0c150369e15d94ccabb95f8dc3b8d26;hb=96b36196d49a3d1f6bc49a26a9d2aa2da7ff876e;hp=e081279489deb949427f30c5208cec0f8bb50290;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index e081279..da997c1 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -21,59 +21,65 @@ ParsimonyCommand::ParsimonyCommand(string option) { else { //valid paramters for this command - string Array[] = {"random","groups","iters"}; + string Array[] = {"random","groups","iters","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - parser = new OptionParser(); - parser->parse(option, parameters); delete parser; + OptionParser parser(option); + map 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::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 = ""; } + 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; } + mothurOut("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."); mothurOutEndLine(); abort = true; } } - + + //if the user changes the output directory command factory will send this info to us in the output parameter + string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } + //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 = ""; } + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; globaldata->Groups.clear(); } 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; - + 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"; + + if(outputDir == "") { outputDir += hasPath(globaldata->getTreeFile()); } + output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString); + + sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary"; openOutputFile(sumFile, outSum); }else { //user wants random distribution savetmap = globaldata->gTreemap; getUserInput(); - output = new ColumnFile(randomtree, itersString); + + if(outputDir == "") { outputDir += hasPath(randomtree); } + output = new ColumnFile(outputDir+ getSimpleName(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->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze util->getCombos(groupComb, globaldata->Groups, numComp); if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); } @@ -87,11 +93,7 @@ ParsimonyCommand::ParsimonyCommand(string option) { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function ParsimonyCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); exit(1); } } @@ -100,24 +102,20 @@ ParsimonyCommand::ParsimonyCommand(string option) { 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"; + mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n"); + mothurOut("The parsimony command parameters are random, groups and iters. 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 parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n"); + mothurOut("Example parsimony(random=out, iters=500).\n"); + mothurOut("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"); + mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n"); + mothurOut("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"; + errorOut(e, "ParsimonyCommand", "help"); 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); - } } @@ -149,7 +147,7 @@ int ParsimonyCommand::execute() { for(int k = 0; k < numComp; k++) { //update uscoreFreq - it = uscoreFreq[k].find(userData[k]); + map::iterator it = uscoreFreq[k].find(userData[k]); if (it == uscoreFreq[k].end()) {//new score uscoreFreq[k][userData[k]] = 1; }else{ uscoreFreq[k][userData[k]]++; } @@ -175,8 +173,8 @@ int ParsimonyCommand::execute() { 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::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; @@ -206,8 +204,8 @@ int ParsimonyCommand::execute() { 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::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; @@ -228,9 +226,9 @@ int ParsimonyCommand::execute() { 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::iterator it = validScores.begin(); it != validScores.end(); it++) { if (randomtree == "") { - it2 = uscoreFreq[a].find(it->first); + map::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 @@ -239,7 +237,7 @@ int ParsimonyCommand::execute() { } //make rscoreFreq map and rCumul - it2 = rscoreFreq[a].find(it->first); + map::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 @@ -274,11 +272,7 @@ int ParsimonyCommand::execute() { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "ParsimonyCommand", "execute"); exit(1); } } @@ -298,7 +292,7 @@ void ParsimonyCommand::printParsimonyFile() { 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::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{ @@ -311,11 +305,7 @@ void ParsimonyCommand::printParsimonyFile() { } } 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"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function printParsimonyFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "ParsimonyCommand", "printParsimonyFile"); exit(1); } } @@ -324,7 +314,7 @@ void ParsimonyCommand::printUSummaryFile() { try { //column headers outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; - cout << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; + mothurOut("Tree#\tGroups\tParsScore\tParsSig"); mothurOutEndLine(); //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -336,9 +326,11 @@ void ParsimonyCommand::printUSummaryFile() { if (UScoreSig[a][i] > (1/(float)iters)) { 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; + mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); mothurOutEndLine(); }else { 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; + mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); mothurOutEndLine(); } } } @@ -346,11 +338,7 @@ void ParsimonyCommand::printUSummaryFile() { outSum.close(); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function printUSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "ParsimonyCommand", "printUSummaryFile"); exit(1); } } @@ -362,16 +350,18 @@ void ParsimonyCommand::getUserInput() { //create treemap tmap = new TreeMap(); - cout << "Please enter the number of groups you would like to analyze: "; + mothurOut("Please enter the number of groups you would like to analyze: "); cin >> numGroups; - + mothurOutJustToLog(toString(numGroups)); mothurOutEndLine(); + int num, count; count = 1; numEachGroup.resize(numGroups, 0); for (int i = 1; i <= numGroups; i++) { - cout << "Please enter the number of sequences in group " << i << ": "; + mothurOut("Please enter the number of sequences in group " + toString(i) + ": "); cin >> num; + mothurOutJustToLog(toString(num)); mothurOutEndLine(); //set tmaps seqsPerGroup tmap->seqsPerGroup[toString(i)] = num; @@ -397,11 +387,7 @@ void ParsimonyCommand::getUserInput() { } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the ParsimonyCommand class function getUserInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + errorOut(e, "ParsimonyCommand", "getUserInput"); exit(1); } }