X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=f092b0f2cf03c8e00d70e437af2219ad9c8def44;hb=438aa88dbc092d9c1c80ec3fa20c8e47f97101c4;hp=f9cdd5a86458c6f3039e4392e6e8b27f7d5eaa08;hpb=d5bf2c1354d0811a33394d918b15620606560d58;p=mothur.git diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp index f9cdd5a..f092b0f 100644 --- a/unifracweightedcommand.cpp +++ b/unifracweightedcommand.cpp @@ -15,13 +15,13 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { 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[] = {"groups","iters","distance","random"}; + string Array[] = {"groups","iters","distance","random","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -35,8 +35,14 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { } if (globaldata->gTree.size() == 0) {//no trees were read - mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); mothurOutEndLine(); abort = true; } - + m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true; } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = ""; + outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } + //check for optional parameter and set defaults // ...at some point should added some additional type checking... groups = validParameter.validFile(parameters, "groups", false); @@ -61,8 +67,9 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { if (abort == false) { T = globaldata->gTree; tmap = globaldata->gTreemap; - sumFile = globaldata->getTreeFile() + ".wsummary"; + sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".wsummary"; openOutputFile(sumFile, outSum); + outputNames.push_back(sumFile); util = new SharedUtil(); string s; //to make work with setgroups @@ -77,7 +84,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { } catch(exception& e) { - errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand"); + m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand"); exit(1); } } @@ -85,20 +92,20 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) { void UnifracWeightedCommand::help(){ try { - mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n"); - mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random. 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 2 valid groups.\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 distance parameter allows you to create a distance file from the results. The default is false.\n"); - mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n"); - mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n"); - mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n"); - mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n"); - mothurOut("The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\n"); - mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); + m->mothurOut("The unifrac.weighted command can only be executed after a successful read.tree command.\n"); + m->mothurOut("The unifrac.weighted command parameters are groups, iters, distance and random. 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 2 valid groups.\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 distance parameter allows you to create a distance file from the results. The default is false.\n"); + m->mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n"); + m->mothurOut("The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters).\n"); + m->mothurOut("Example unifrac.weighted(groups=A-B-C, iters=500).\n"); + m->mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n"); + m->mothurOut("The unifrac.weighted command output two files: .weighted and .wsummary their descriptions are in the manual.\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); } catch(exception& e) { - errorOut(e, "UnifracWeightedCommand", "help"); + m->errorOut(e, "UnifracWeightedCommand", "help"); exit(1); } } @@ -121,14 +128,35 @@ int UnifracWeightedCommand::execute() { //get weighted scores for users trees for (int i = 0; i < T.size(); i++) { + + if (m->control_pressed) { + delete randT; + if (random) { delete reading; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + counter = 0; rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... uScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC... - if (random) { output = new ColumnFile(globaldata->getTreeFile() + toString(i+1) + ".weighted", itersString); } + if (random) { + output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted", itersString); + outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted"); + } userData = weighted->getValues(T[i]); //userData[0] = weightedscore + if (m->control_pressed) { + delete randT; + if (random) { delete reading; delete output; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + //save users score for (int s=0; sassembleRandomUnifracTree(globaldata->Groups[r], globaldata->Groups[l]); + + if (m->control_pressed) { + delete randT; + if (random) { delete reading; delete output; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + + //get wscore of random tree randomData = weighted->getValues(randT, globaldata->Groups[r], globaldata->Groups[l]); + if (m->control_pressed) { + delete randT; + if (random) { delete reading; delete output; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + //save scores rScores[count].push_back(randomData[0]); count++; @@ -173,7 +219,7 @@ int UnifracWeightedCommand::execute() { //so if you have 1000 random trees the index returned is 100 //then there are 900 trees with a score greater then you. //giving you a signifigance of 0.900 - int index = findIndex(userData[f], f); if (index == -1) { mothurOut("error in UnifracWeightedCommand"); mothurOutEndLine(); exit(1); } //error code + int index = findIndex(userData[f], f); if (index == -1) { m->mothurOut("error in UnifracWeightedCommand"); m->mothurOutEndLine(); exit(1); } //error code //the signifigance is the number of trees with the users score or higher WScoreSig.push_back((iters-index)/(float)iters); @@ -192,6 +238,15 @@ int UnifracWeightedCommand::execute() { validScores.clear(); } + + if (m->control_pressed) { + delete randT; + if (random) { delete reading; } + outSum.close(); + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + return 0; + } + //finish progress bar if (random) { reading->finish(); delete reading; } @@ -204,11 +259,21 @@ int UnifracWeightedCommand::execute() { delete randT; + if (m->control_pressed) { + for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } + 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) { - errorOut(e, "UnifracWeightedCommand", "execute"); + m->errorOut(e, "UnifracWeightedCommand", "execute"); exit(1); } } @@ -231,7 +296,7 @@ void UnifracWeightedCommand::printWeightedFile() { } } catch(exception& e) { - errorOut(e, "UnifracWeightedCommand", "printWeightedFile"); + m->errorOut(e, "UnifracWeightedCommand", "printWeightedFile"); exit(1); } } @@ -242,7 +307,7 @@ void UnifracWeightedCommand::printWSummaryFile() { try { //column headers outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" << endl; - mothurOut("Tree#\tGroups\tWScore\tWSig"); mothurOutEndLine(); + m->mothurOut("Tree#\tGroups\tWScore\tWSig"); m->mothurOutEndLine(); //format output outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint); @@ -255,16 +320,16 @@ void UnifracWeightedCommand::printWSummaryFile() { if (WScoreSig[count] > (1/(float)iters)) { outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl; cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl; - mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); mothurOutEndLine(); + m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); m->mothurOutEndLine(); }else{ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl; - mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); mothurOutEndLine(); + m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); m->mothurOutEndLine(); } }else{ outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl; cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl; - mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); mothurOutEndLine(); + m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); m->mothurOutEndLine(); } count++; } @@ -272,7 +337,7 @@ void UnifracWeightedCommand::printWSummaryFile() { outSum.close(); } catch(exception& e) { - errorOut(e, "UnifracWeightedCommand", "printWSummaryFile"); + m->errorOut(e, "UnifracWeightedCommand", "printWSummaryFile"); exit(1); } } @@ -283,7 +348,8 @@ void UnifracWeightedCommand::createPhylipFile() { //for each tree for (int i = 0; i < T.size(); i++) { - string phylipFileName = globaldata->getTreeFile() + toString(i+1) + ".weighted.dist"; + string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile()) + toString(i+1) + ".weighted.dist"; + outputNames.push_back(phylipFileName); ofstream out; openOutputFile(phylipFileName, out); @@ -299,8 +365,8 @@ void UnifracWeightedCommand::createPhylipFile() { //flip it so you can print it for (int r=0; rGroups.size(); r++) { for (int l = r+1; l < globaldata->Groups.size(); l++) { - dists[r][l] = (1.0 - utreeScores[count]); - dists[l][r] = (1.0 - utreeScores[count]); + dists[r][l] = utreeScores[count]; + dists[l][r] = utreeScores[count]; count++; } } @@ -308,7 +374,11 @@ void UnifracWeightedCommand::createPhylipFile() { //output to file for (int r=0; rGroups.size(); r++) { //output name - out << globaldata->Groups[r] << '\t'; + string name = globaldata->Groups[r]; + if (name.length() < 10) { //pad with spaces to make compatible + while (name.length() < 10) { name += " "; } + } + out << name << '\t'; //output distances for (int l = 0; l < r; l++) { out << dists[r][l] << '\t'; } @@ -318,7 +388,7 @@ void UnifracWeightedCommand::createPhylipFile() { } } catch(exception& e) { - errorOut(e, "UnifracWeightedCommand", "createPhylipFile"); + m->errorOut(e, "UnifracWeightedCommand", "createPhylipFile"); exit(1); } } @@ -331,7 +401,7 @@ int UnifracWeightedCommand::findIndex(float score, int index) { return rScores[index].size(); } catch(exception& e) { - errorOut(e, "UnifracWeightedCommand", "findIndex"); + m->errorOut(e, "UnifracWeightedCommand", "findIndex"); exit(1); } } @@ -376,7 +446,7 @@ void UnifracWeightedCommand::calculateFreqsCumuls() { } catch(exception& e) { - errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums"); + m->errorOut(e, "UnifracWeightedCommand", "calculateFreqsCums"); exit(1); } }