X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=c97e92ed7253cf1cdf00882a6e1155c1b86fe60a;hb=e99751591aa21705e58edda87383457b9738dd9e;hp=266dd3b9a2ad5c3e7730ac6950e7077164b12bb2;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index 266dd3b..c97e92e 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -9,19 +9,67 @@ #include "parsimonycommand.h" +//********************************************************************************************************************** +vector ParsimonyCommand::getValidParameters(){ + try { + string Array[] = {"random","groups","iters","processors","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +ParsimonyCommand::ParsimonyCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["parsimony"] = tempOutNames; + outputTypes["psummary"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector ParsimonyCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ParsimonyCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ParsimonyCommand", "getRequiredFiles"); + exit(1); + } +} /***********************************************************/ -ParsimonyCommand::ParsimonyCommand(string option) { +ParsimonyCommand::ParsimonyCommand(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[] = {"random","groups","iters"}; + string Array[] = {"random","groups","processors","iters","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -34,25 +82,36 @@ ParsimonyCommand::ParsimonyCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["parsimony"] = tempOutNames; + outputTypes["psummary"] = tempOutNames; + 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; } + m->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."); m->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 = ""; if (randomtree == "") { outputDir += m->hasPath(globaldata->inputFileName); } } + //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 = ""; } + if (groups == "not found") { groups = ""; globaldata->Groups.clear(); } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; } convert(itersString, iters); + + string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + convert(temp, processors); if (abort == false) { //randomtree will tell us if user had their own treefile or if they just want the random distribution @@ -60,18 +119,29 @@ ParsimonyCommand::ParsimonyCommand(string option) { if (randomtree == "") { T = globaldata->gTree; tmap = globaldata->gTreemap; - output = new ColumnFile(globaldata->getTreeFile() + ".parsimony", itersString); - sumFile = globaldata->getTreeFile() + ".psummary"; - openOutputFile(sumFile, outSum); + + if(outputDir == "") { outputDir += m->hasPath(globaldata->getTreeFile()); } + output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony", itersString); + outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony"); + outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".parsimony"); + + sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".psummary"; + m->openOutputFile(sumFile, outSum); + outputNames.push_back(sumFile); + outputTypes["psummary"].push_back(sumFile); }else { //user wants random distribution savetmap = globaldata->gTreemap; getUserInput(); - output = new ColumnFile(randomtree, itersString); + + if(outputDir == "") { outputDir += m->hasPath(randomtree); } + output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString); + outputNames.push_back(outputDir+ m->getSimpleName(randomtree)); + outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree)); } //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); } @@ -85,11 +155,7 @@ 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"; + m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); exit(1); } } @@ -98,24 +164,21 @@ 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"; + m->mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n"); + m->mothurOut("The parsimony command parameters are random, groups, processors and iters. No parameters are required.\n"); + m->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"); + m->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"); + m->mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n"); + m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); + m->mothurOut("Example parsimony(random=out, iters=500).\n"); + m->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"); + m->mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n"); + m->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"; + m->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); - } } @@ -128,6 +191,15 @@ int ParsimonyCommand::execute() { Progress* reading; reading = new Progress("Comparing to random:", iters); + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + globaldata->Groups.clear(); + return 0; + } + + //get pscore for users tree userData.resize(numComp,0); //data = AB, AC, BC, ABC. randomData.resize(numComp,0); //data = AB, AC, BC, ABC. @@ -141,7 +213,16 @@ int ParsimonyCommand::execute() { if (randomtree == "") { //get pscores for users trees for (int i = 0; i < T.size(); i++) { - userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC. + userData = pars->getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC. + + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + globaldata->Groups.clear(); + return 0; + } + //output scores for each combination for(int k = 0; k < numComp; k++) { @@ -162,6 +243,7 @@ int ParsimonyCommand::execute() { //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(); @@ -169,7 +251,15 @@ int ParsimonyCommand::execute() { randT->assembleRandomTree(); //get pscore of random tree - randomData = pars->getValues(randT); + randomData = pars->getValues(randT, processors, outputDir); + + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; delete randT; + if (randomtree == "") { outSum.close(); } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + globaldata->Groups.clear(); + return 0; + } for(int r = 0; r < numComp; r++) { //add trees pscore to map of scores @@ -193,14 +283,32 @@ int ParsimonyCommand::execute() { }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(); + + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; delete randT; + globaldata->gTreemap = savetmap; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + globaldata->Groups.clear(); + return 0; + } + //get pscore of random tree - randomData = pars->getValues(randT); + randomData = pars->getValues(randT, processors, outputDir); + + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; delete randT; + globaldata->gTreemap = savetmap; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + globaldata->Groups.clear(); + return 0; + } for(int r = 0; r < numComp; r++) { //add trees pscore to map of scores @@ -250,6 +358,15 @@ int ParsimonyCommand::execute() { } } + if (m->control_pressed) { + delete reading; delete pars; delete util; delete output; + if (randomtree == "") { outSum.close(); } + else { globaldata->gTreemap = savetmap; } + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + globaldata->Groups.clear(); + return 0; + } + //finish progress bar reading->finish(); delete reading; @@ -268,15 +385,23 @@ int ParsimonyCommand::execute() { //reset groups parameter globaldata->Groups.clear(); + if (m->control_pressed) { + delete pars; delete util; delete output; + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + return 0; + } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + + return 0; } 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"; + m->errorOut(e, "ParsimonyCommand", "execute"); exit(1); } } @@ -309,20 +434,16 @@ 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"; + m->errorOut(e, "ParsimonyCommand", "printParsimonyFile"); exit(1); } } /***********************************************************/ -void ParsimonyCommand::printUSummaryFile() { +int ParsimonyCommand::printUSummaryFile() { try { //column headers outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; - cout << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; + m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine(); //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -331,24 +452,24 @@ void ParsimonyCommand::printUSummaryFile() { //print each line for (int i = 0; i< T.size(); i++) { for(int a = 0; a < numComp; a++) { + if (m->control_pressed) { outSum.close(); return 0; } 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; + m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString(UScoreSig[a][i])); m->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; + m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine(); } } } outSum.close(); + return 0; } 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"; + m->errorOut(e, "ParsimonyCommand", "printUSummaryFile"); exit(1); } } @@ -360,16 +481,18 @@ void ParsimonyCommand::getUserInput() { //create treemap tmap = new TreeMap(); - cout << "Please enter the number of groups you would like to analyze: "; + m->mothurOut("Please enter the number of groups you would like to analyze: "); cin >> numGroups; - + m->mothurOutJustToLog(toString(numGroups)); m->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 << ": "; + m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": "); cin >> num; + m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine(); //set tmaps seqsPerGroup tmap->seqsPerGroup[toString(i)] = num; @@ -395,11 +518,7 @@ 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"; + m->errorOut(e, "ParsimonyCommand", "getUserInput"); exit(1); } }