X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=393c0f8930eac7649ba18f0dc7db344ed9ebed56;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=6ffb30b3caf18a695604c69c5556b2b7c5c2b50a;hpb=5a9f3cce3e2e053c249e3e97507ce180f0854d76;p=mothur.git diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp index 6ffb30b..393c0f8 100644 --- a/parsimonycommand.cpp +++ b/parsimonycommand.cpp @@ -10,18 +10,18 @@ #include "parsimonycommand.h" /***********************************************************/ -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","iters","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -39,9 +39,12 @@ 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) { - 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; } + 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 = ""; } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... groups = validParameter.validFile(parameters, "groups", false); @@ -60,13 +63,21 @@ 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); + outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + ".parsimony"); + + sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary"; openOutputFile(sumFile, outSum); + outputNames.push_back(sumFile); }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); + outputNames.push_back(outputDir+ getSimpleName(randomtree)); } //set users groups to analyze @@ -85,7 +96,7 @@ ParsimonyCommand::ParsimonyCommand(string option) { } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); + m->errorOut(e, "ParsimonyCommand", "ParsimonyCommand"); exit(1); } } @@ -94,18 +105,18 @@ ParsimonyCommand::ParsimonyCommand(string option) { void ParsimonyCommand::help(){ try { - 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"); + 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 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("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) { - errorOut(e, "ParsimonyCommand", "help"); + m->errorOut(e, "ParsimonyCommand", "help"); exit(1); } } @@ -260,11 +271,17 @@ int ParsimonyCommand::execute() { //reset groups parameter globaldata->Groups.clear(); + 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) { - errorOut(e, "ParsimonyCommand", "execute"); + m->errorOut(e, "ParsimonyCommand", "execute"); exit(1); } } @@ -297,7 +314,7 @@ void ParsimonyCommand::printParsimonyFile() { } } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "printParsimonyFile"); + m->errorOut(e, "ParsimonyCommand", "printParsimonyFile"); exit(1); } } @@ -306,7 +323,7 @@ void ParsimonyCommand::printUSummaryFile() { try { //column headers outSum << "Tree#" << '\t' << "Groups" << '\t' << "ParsScore" << '\t' << "ParsSig" << endl; - mothurOut("Tree#\tGroups\tParsScore\tParsSig"); mothurOutEndLine(); + m->mothurOut("Tree#\tGroups\tParsScore\tParsSig"); m->mothurOutEndLine(); //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -318,11 +335,11 @@ 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(); + 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; - mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); mothurOutEndLine(); + m->mothurOutJustToLog(toString(i+1) + "\t" + groupComb[a] + "\t" + toString(userTreeScores[a][i]) + "\t" + toString((1/float(iters)))); m->mothurOutEndLine(); } } } @@ -330,7 +347,7 @@ void ParsimonyCommand::printUSummaryFile() { outSum.close(); } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "printUSummaryFile"); + m->errorOut(e, "ParsimonyCommand", "printUSummaryFile"); exit(1); } } @@ -342,18 +359,18 @@ void ParsimonyCommand::getUserInput() { //create treemap tmap = new TreeMap(); - mothurOut("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; - mothurOutJustToLog(toString(numGroups)); mothurOutEndLine(); + m->mothurOutJustToLog(toString(numGroups)); m->mothurOutEndLine(); int num, count; count = 1; numEachGroup.resize(numGroups, 0); for (int i = 1; i <= numGroups; i++) { - mothurOut("Please enter the number of sequences in group " + toString(i) + ": "); + m->mothurOut("Please enter the number of sequences in group " + toString(i) + ": "); cin >> num; - mothurOutJustToLog(toString(num)); mothurOutEndLine(); + m->mothurOutJustToLog(toString(num)); m->mothurOutEndLine(); //set tmaps seqsPerGroup tmap->seqsPerGroup[toString(i)] = num; @@ -379,7 +396,7 @@ void ParsimonyCommand::getUserInput() { } catch(exception& e) { - errorOut(e, "ParsimonyCommand", "getUserInput"); + m->errorOut(e, "ParsimonyCommand", "getUserInput"); exit(1); } }