X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=da997c13b0c150369e15d94ccabb95f8dc3b8d26;hb=5f44783e6d74a9c207492ac244210c915cadc272;hp=266dd3b9a2ad5c3e7730ac6950e7077164b12bb2;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index 266dd3b..da997c1 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -21,7 +21,7 @@ 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))); OptionParser parser(option); @@ -39,13 +39,16 @@ ParsimonyCommand::ParsimonyCommand(string option) { //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 = ""; } + if (groups == "not found") { groups = ""; globaldata->Groups.clear(); } else { splitAtDash(groups, Groups); globaldata->Groups = Groups; @@ -60,18 +63,23 @@ ParsimonyCommand::ParsimonyCommand(string option) { 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); } @@ -85,11 +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); } } @@ -98,24 +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); - } } @@ -272,11 +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); } } @@ -309,11 +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); } } @@ -322,7 +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); @@ -334,9 +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(); } } } @@ -344,11 +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); } } @@ -360,16 +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; @@ -395,11 +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); } }